6 Differential Expression Analysis I
6.1 Joint analysis of all samples
For the global differential expression analysis, samples from Batches 1 and 2 were analyzed jointly, as both were processed under comparable experimental and sequencing conditions.
The overall distribution of median gene expression values showed that most genes were expressed at low levels across samples, with a steep drop in frequency toward higher expression values. Only a small subset of genes displayed high expression (log₁₀ > 4), consistent with the typical right-skewed distribution of RNA-seq count data. This confirmed that lowly expressed and noise-dominated genes dominated the raw dataset prior to filtering and normalization.
Genes with very low read counts were excluded to minimize technical noise. After filtering for a minimum of 20 counts in at least five samples, approximately 19011 genes were retained for downstream analysis.
Filtering removes genes with little information (low counts / expressed in few samples), which stabilizes dispersion estimates and multiple‑testing behavior.
The choice of cutoff (20 counts, ≥5 samples) is arbitrary
6.1.1 Liver
6.1.1.1 All mice (male and females)
There are 346 significantly differentially expressed genes (FDR < 0.01, |log2FC| > 1) in the liver between Cre-AAV and GFP control switch mice.
Diagnostic plots for the DE analysis
- A histogram enriched for low p-values shows the presence of true differential expression (deviation from the uniform null), rather than an all-noise result.
- The log(baseMean) distribution for significant genes being skewed toward moderate–high counts indicates findings are driven by well-expressed features, not low-count noise that can inflate fold-changes and p-values.
Significantly differentially expressed genes in liver
Cre-AAV and GFP control
(FDR < 0.01, |log2FC| > 1)
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Gstm2-ps1 | 52.13 | -3.85 | 0.00 |
| Vcp-rs | 62.44 | -3.22 | 0.00 |
| Rpl35a-ps2 | 28.38 | -23.87 | 0.00 |
| Gm10073 | 32.44 | -3.86 | 0.00 |
| Gm10263 | 16.80 | -5.51 | 0.00 |
| Gm45855 | 30.89 | -2.76 | 0.00 |
| Rpl18-ps2 | 28.35 | -3.97 | 0.00 |
| Gm4332 | 34.81 | -3.75 | 0.00 |
| Gm8730 | 49.37 | -3.49 | 0.00 |
| Gm11478 | 47.92 | -3.35 | 0.00 |
| Gm6548 | 80.08 | -1.26 | 0.00 |
| ENSMUSG00000143433 | 27.62 | -3.89 | 0.00 |
| Gm8566 | 103.10 | -3.30 | 0.00 |
| ENSMUSG00000121793 | 103.54 | -2.85 | 0.00 |
| Gm4366 | 55.30 | -2.36 | 0.00 |
| Rpl28-ps1 | 55.38 | -3.03 | 0.00 |
| ENSMUSG00000135866 | 244.14 | -3.77 | 0.00 |
| Gm13436 | 30.54 | -3.84 | 0.00 |
| Eef2-ps2 | 24.97 | -3.75 | 0.00 |
| Glns-ps1 | 27.95 | -3.44 | 0.00 |
| Ntn3 | 95.27 | -1.12 | 0.00 |
| Gm16437 | 14.49 | -3.72 | 0.00 |
| Gm14586 | 41.69 | -3.27 | 0.00 |
| Gm15163 | 37.44 | -2.75 | 0.00 |
| Gm10221 | 36.85 | -3.01 | 0.00 |
| Lrp1 | 8347.24 | -1.05 | 0.00 |
| Glo1-ps | 42.32 | -2.76 | 0.00 |
| Rps16-ps2 | 76.01 | -2.79 | 0.00 |
| mt-Ts1 | 8.25 | -6.64 | 0.00 |
| Gm9816 | 16.07 | -3.07 | 0.00 |
| Gm10076 | 1650.81 | 1.18 | 0.00 |
| Got2-ps1 | 56.74 | -1.80 | 0.00 |
| Gm6204 | 31.50 | -3.78 | 0.00 |
| Gm10232 | 15.00 | -3.22 | 0.00 |
| Ccdc148 | 70.68 | 1.20 | 0.00 |
| Ftl1-ps1 | 496.94 | -2.43 | 0.00 |
| Gm5540 | 31.75 | -3.03 | 0.00 |
| Cox5b-ps | 35.84 | -2.60 | 0.00 |
| Gm13611 | 12.34 | -5.37 | 0.00 |
| Gm5805 | 13.37 | -4.11 | 0.00 |
| Gm28437 | 94444.19 | 1.10 | 0.00 |
| Gm4149 | 33.43 | -3.11 | 0.00 |
| Gm9794 | 71.29 | -2.36 | 0.00 |
| Rpl17-ps3 | 54.82 | -2.66 | 0.00 |
| Gm12174 | 25.91 | -2.88 | 0.00 |
| Gm9625 | 27.50 | -2.69 | 0.00 |
| Gm12350 | 32.72 | -2.86 | 0.00 |
| Gm8355 | 42.47 | -2.18 | 0.00 |
| Gm9755 | 20.01 | -3.02 | 0.00 |
| Rps18-ps5 | 43.48 | -3.87 | 0.00 |
| Rps26-ps1 | 18.09 | -7.78 | 0.00 |
| Gm7536 | 114.42 | -2.11 | 0.00 |
| Rps3a2 | 74.27 | -2.29 | 0.00 |
| Rps19-ps6 | 40.54 | -2.87 | 0.00 |
| Hspe1-rs1 | 36.98 | -2.60 | 0.00 |
| Rpl19-ps11 | 106.16 | -2.18 | 0.00 |
| ENSMUSG00000128633 | 88.57 | -3.28 | 0.00 |
| Rps23-ps1 | 53.86 | -2.32 | 0.00 |
| Gm2962 | 11.36 | -3.15 | 0.00 |
| Gm12481 | 52.24 | -6.63 | 0.00 |
| Rpsa-ps10 | 82.60 | -2.28 | 0.00 |
| Rpl34-ps1 | 51.23 | -4.30 | 0.00 |
| Llph-ps2 | 179.22 | 1.13 | 0.00 |
| Gm7049 | 17.26 | -3.02 | 0.00 |
| Gm5835 | 25.57 | -2.69 | 0.00 |
| Oaz1-ps | 127.45 | -2.23 | 0.00 |
| Uba52rt | 196.86 | -1.83 | 0.00 |
| Gm5422 | 13.06 | -3.51 | 0.00 |
| Gm6652 | 265.61 | -1.49 | 0.00 |
| Rpl7-ps7 | 12.28 | -2.63 | 0.00 |
| Sap18b | 36.69 | -2.14 | 0.00 |
| Akap17a | 203.34 | -1.21 | 0.00 |
| Gm12918 | 83.49 | -2.36 | 0.00 |
| Gm10288 | 109.88 | -2.66 | 0.00 |
| Rpl35rt | 116.67 | -2.74 | 0.00 |
| Eno1b | 36.85 | -3.70 | 0.00 |
| Rpl23a-ps3 | 32.26 | -2.57 | 0.00 |
| Gm7600 | 15.99 | -3.59 | 0.00 |
| Gm10874 | 21.01 | -2.43 | 0.00 |
| ENSMUSG00000126438 | 14.28 | -3.17 | 0.00 |
| Glud-ps | 36.25 | -2.37 | 0.00 |
| ENSMUSG00000139771 | 162.30 | -2.77 | 0.00 |
| mt-Nd6 | 26837.91 | 1.17 | 0.00 |
| Gm11964 | 10.20 | -3.94 | 0.00 |
| Adrm1b | 35.04 | -2.70 | 0.00 |
| Tpt1-ps3 | 139.00 | -2.08 | 0.00 |
| Gm10039 | 19.90 | -2.65 | 0.00 |
| Gm5456 | 15.55 | -3.66 | 0.00 |
| Mif-ps4 | 9.04 | -4.81 | 0.00 |
| Eif4a-ps4 | 98.87 | -1.64 | 0.00 |
| Gm4459 | 14.26 | -3.34 | 0.00 |
| Gm10250 | 43.21 | -2.52 | 0.00 |
| Gm12183 | 24.33 | -2.54 | 0.00 |
| Gm12251 | 15.42 | -2.70 | 0.00 |
| Gm21399 | 55.48 | -2.09 | 0.00 |
| ENSMUSG00000132147 | 63.59 | -2.52 | 0.00 |
| ENSMUSG00000137224 | 123.65 | -1.65 | 0.00 |
| Gm6863 | 63.19 | -1.88 | 0.00 |
| Rpl6l | 21.24 | -2.03 | 0.00 |
| Rps15-ps2 | 7.66 | -3.79 | 0.00 |
| Gm15772 | 25.60 | -2.69 | 0.00 |
| Gm6733 | 14.92 | -2.76 | 0.00 |
| Ap2m1-ps | 53.09 | -1.93 | 0.00 |
| Rps10-ps1 | 15.37 | -3.88 | 0.00 |
| Abca2 | 551.64 | -1.28 | 0.00 |
| Gm10163 | 31.62 | -2.42 | 0.00 |
| Pgam1-ps2 | 23.48 | -2.62 | 0.00 |
| Gm9616 | 13.98 | -2.96 | 0.00 |
| Gm15427 | 76.23 | -2.77 | 0.00 |
| Hspd1-ps3 | 55.65 | -1.85 | 0.00 |
| Gm7658 | 12.59 | -2.57 | 0.00 |
| Gm10053 | 99.63 | -2.26 | 0.00 |
| ENSMUSG00000131289 | 19.95 | -2.81 | 0.00 |
| Gm5560 | 20.73 | -2.38 | 0.00 |
| Gpi-ps | 16.57 | -2.79 | 0.00 |
| Gm5452 | 24.48 | -2.73 | 0.00 |
| Gm6180 | 6.74 | -3.44 | 0.00 |
| Gm6170 | 11.84 | -2.94 | 0.00 |
| Rps25-ps1 | 15.45 | -3.02 | 0.00 |
| Gm9385 | 49.90 | -2.63 | 0.00 |
| Rps27a-ps2 | 53.04 | -1.80 | 0.00 |
| Gm7666 | 39.32 | -2.39 | 0.00 |
| Abca3 | 1133.90 | -1.00 | 0.00 |
| Gm37035 | 190.24 | -1.00 | 0.00 |
| Rpl14-ps1 | 52.91 | -1.94 | 0.00 |
| mt-Nd5 | 125169.00 | 1.02 | 0.00 |
| Rps18-ps6 | 75.96 | -2.62 | 0.00 |
| ENSMUSG00000132604 | 23.58 | -3.13 | 0.00 |
| Gm28661 | 135299.60 | 1.02 | 0.00 |
| Pam16l | 10.60 | -2.62 | 0.00 |
| Ndufb4c | 283.83 | 1.04 | 0.00 |
| Gm16439 | 37.11 | -2.33 | 0.00 |
| Gm12346 | 20.50 | -2.19 | 0.00 |
| Ptprf | 2352.48 | -1.07 | 0.00 |
| Gm44170 | 66.86 | -2.04 | 0.00 |
| Rab11b-ps2 | 4.76 | -4.18 | 0.00 |
| Gm9892 | 20.33 | -1.89 | 0.00 |
| Gm7816 | 22.48 | -2.25 | 0.00 |
| Gm13461 | 11.64 | -2.72 | 0.00 |
| Gm7336 | 369.13 | -1.11 | 0.00 |
| Gm6055 | 9.53 | -2.34 | 0.00 |
| Gm7730 | 10.33 | -3.42 | 0.00 |
| Rpl31-ps8 | 41.91 | -1.80 | 0.00 |
| Fn1 | 19461.02 | -1.02 | 0.00 |
| Gm9826 | 135.93 | -2.26 | 0.00 |
| Gm5424 | 947.45 | -1.97 | 0.00 |
| ENSMUSG00000126686 | 64.44 | 1.11 | 0.00 |
| Gm13456 | 473.36 | -1.91 | 0.00 |
| Tpm3-rs7 | 18.97 | -1.95 | 0.00 |
| ENSMUSG00000130204 | 43.03 | -1.68 | 0.00 |
| Gm6789 | 99.15 | -1.63 | 0.00 |
| Gm7204 | 18.21 | -2.05 | 0.00 |
| Gm13680 | 15.05 | -2.66 | 0.00 |
| Hadhb-ps | 140.94 | -1.56 | 0.00 |
| ENSMUSG00000132256 | 10.60 | -2.77 | 0.00 |
| Gm2225 | 9.96 | -2.66 | 0.00 |
| Eif3j2 | 60.64 | -1.70 | 0.00 |
| Gm9493 | 34.64 | -2.14 | 0.00 |
| ENSMUSG00000125136 | 7.80 | -2.42 | 0.00 |
| Atp6v0c-ps2 | 7.96 | -2.29 | 0.00 |
| ENSMUSG00000123407 | 9.32 | -3.27 | 0.00 |
| Nphs1 | 4.88 | 3.13 | 0.00 |
| Rpl17-ps10 | 73.91 | -1.90 | 0.00 |
| Gm5499 | 5.05 | -3.18 | 0.00 |
| Gm6136 | 60.21 | -1.64 | 0.00 |
| ENSMUSG00000122915 | 12.16 | -3.41 | 0.00 |
| Tmppe | 31.49 | -1.00 | 0.00 |
| Kpna2rt | 15.98 | -2.27 | 0.00 |
| Gm10819 | 6.88 | -3.14 | 0.00 |
| Rps6-ps4 | 144.91 | -1.48 | 0.00 |
| Gm5182 | 10.02 | -2.79 | 0.00 |
| Actr3-ps | 10.09 | -2.27 | 0.00 |
| Gm57504 | 13.10 | -1.79 | 0.00 |
| Mmp15 | 522.08 | -1.23 | 0.00 |
| AK157302 | 6.50 | -3.00 | 0.00 |
| Rpl9-ps4 | 20.50 | -2.22 | 0.00 |
| Mrpl23-ps1 | 12.34 | -2.36 | 0.00 |
| Gm8203 | 6.24 | -3.24 | 0.00 |
| Wdr89 | 87.06 | -1.08 | 0.00 |
| Gm4202 | 7.20 | -2.76 | 0.00 |
| Tmed2b | 22.20 | -1.74 | 0.00 |
| Tpi-rs11 | 5.25 | -3.69 | 0.00 |
| ENSMUSG00000140707 | 19.38 | 1.19 | 0.00 |
| ENSMUSG00000125175 | 21.20 | -2.01 | 0.00 |
| Kcp | 52.56 | -1.44 | 0.00 |
| ENSMUSG00000133704 | 22.57 | -1.87 | 0.00 |
| Mov10 | 216.85 | -1.05 | 0.00 |
| Gm20056 | 12.66 | -2.19 | 0.00 |
| Gm6206 | 14.32 | -1.86 | 0.00 |
| Rps24-ps3 | 28.02 | -2.24 | 0.00 |
| Gm10036 | 13.35 | -2.39 | 0.00 |
| Rps10-ps2 | 49.17 | -1.55 | 0.00 |
| ENSMUSG00000121784 | 135.87 | -1.36 | 0.00 |
| Gm12992 | 72.44 | -1.18 | 0.00 |
| ENSMUSG00000128869 | 8.51 | -3.93 | 0.00 |
| Btf3-ps1 | 20.61 | -1.83 | 0.00 |
| Rps15a-ps7 | 16.53 | -2.49 | 0.00 |
| Gm45507 | 179.36 | 1.18 | 0.00 |
| Gm12254 | 24.06 | -1.73 | 0.00 |
| Rps13-ps1 | 33.55 | -2.34 | 0.00 |
| Gm6344 | 12.70 | -2.75 | 0.00 |
| Gm44442 | 273.09 | -1.27 | 0.00 |
| Rpl36a-ps2 | 19.83 | -2.03 | 0.00 |
| Rps2-ps10 | 25.90 | -8.30 | 0.00 |
| Col1a1 | 50.99 | -1.14 | 0.00 |
| Gm5436 | 11.73 | -2.70 | 0.00 |
| Gm12966 | 13.65 | -1.95 | 0.00 |
| Rplp2-ps1 | 25.89 | -3.58 | 0.00 |
| Gm14494 | 11.73 | -2.17 | 0.00 |
| Gm15542 | 55.44 | -1.04 | 0.00 |
| Impdh2-ps | 10.80 | -2.00 | 0.00 |
| Gm10252 | 12357.65 | 1.20 | 0.00 |
| Psma5-ps | 19.33 | -2.05 | 0.00 |
| Mir6236 | 26.56 | -1.80 | 0.00 |
| Gm5421 | 8.23 | -2.68 | 0.00 |
| Gm2223 | 17.68 | -1.81 | 0.00 |
| ENSMUSG00000121777 | 558.33 | -1.39 | 0.00 |
| Nudc-ps1 | 6.65 | -3.03 | 0.00 |
| Gm2614 | 8.27 | -2.86 | 0.00 |
| Hspb1 | 382.47 | -1.06 | 0.00 |
| Gm22009 | 33.05 | 2.72 | 0.00 |
| Rn7s1 | 890.15 | 1.74 | 0.00 |
| Rpl36-ps12 | 39.43 | -1.71 | 0.00 |
| Gm13835 | 78.41 | -1.28 | 0.00 |
| Ahcyl | 1153.38 | -1.36 | 0.00 |
| Ube2srt | 6.21 | -2.80 | 0.00 |
| ENSMUSG00000121655 | 23.67 | -1.91 | 0.00 |
| Gm5905 | 24.65 | -2.00 | 0.00 |
| Gstp-ps | 125.10 | -3.28 | 0.00 |
| Kansl2-ps | 4.89 | -2.21 | 0.00 |
| Nrtn | 24.00 | -1.39 | 0.00 |
| Rpl3-ps1 | 95.37 | -1.26 | 0.00 |
| Rpl15-ps3 | 44.55 | -3.99 | 0.00 |
| Hcn3 | 87.03 | -1.69 | 0.00 |
| Bhmt1b | 952.66 | -1.92 | 0.00 |
| Dmbt1 | 53.46 | 4.28 | 0.00 |
| Gm5884 | 13.14 | -1.24 | 0.00 |
| Gm4633 | 12.02 | 1.15 | 0.00 |
| Fam222a | 32.22 | -1.76 | 0.00 |
| Zbtb42 | 82.80 | -1.04 | 0.00 |
| ENSMUSG00000130316 | 15.04 | -1.26 | 0.00 |
| Pcbp3 | 15.89 | -1.15 | 0.00 |
| ENSMUSG00000123794 | 29.55 | -1.12 | 0.00 |
| Gm15519 | 10.05 | -2.68 | 0.00 |
| Cd28 | 8.33 | 1.42 | 0.00 |
| Atp11a | 291.46 | -1.06 | 0.00 |
| Mxd4os1 | 27.79 | -1.01 | 0.00 |
| Rpsa-ps2 | 9.06 | -2.71 | 0.00 |
| ENSMUSG00000123149 | 23.72 | -1.60 | 0.00 |
| Csnk2a1-ps3 | 22.75 | -1.44 | 0.00 |
| Gm8399 | 6.88 | -2.74 | 0.00 |
| Gm57397 | 11.52 | 1.24 | 0.00 |
| Rps27rt | 157.04 | -1.88 | 0.00 |
| Slc41a2 | 285.10 | -1.73 | 0.00 |
| Gm19918 | 8.67 | -2.16 | 0.00 |
| Gm9531 | 7.57 | -2.05 | 0.00 |
| Rps18-ps3 | 16.40 | -3.70 | 0.00 |
| ENSMUSG00000121644 | 23.40 | -1.17 | 0.00 |
| Gm57204 | 33.56 | 1.17 | 0.00 |
| ENSMUSG00000121608 | 17.33 | -1.51 | 0.00 |
| Mrip-ps | 5.74 | -2.33 | 0.00 |
| Col15a1 | 67.78 | -1.06 | 0.00 |
| ENSMUSG00000124469 | 21.16 | 1.10 | 0.00 |
| P2ry10 | 12.74 | 1.37 | 0.00 |
| ENSMUSG00000128964 | 19.69 | 1.07 | 0.00 |
| Fasn | 2164.04 | -1.70 | 0.00 |
| Apold1 | 61.53 | 1.02 | 0.00 |
| Gadl1 | 7.53 | -2.14 | 0.00 |
| Gm20707 | 8.35 | 1.45 | 0.00 |
| Rpl10a-ps1 | 95.72 | -1.04 | 0.00 |
| Gm2999 | 8.24 | -2.33 | 0.00 |
| Gm28439 | 601.79 | 2.04 | 0.00 |
| Gm3571 | 12.88 | -3.44 | 0.00 |
| Atp5pb-ps | 30.83 | -1.38 | 0.00 |
| Scp2-ps2 | 144.46 | -3.35 | 0.00 |
| 4921516A02Rik | 55.19 | -1.29 | 0.00 |
| ENSMUSG00000141850 | 8.45 | -2.83 | 0.00 |
| Fosb | 22.06 | 2.04 | 0.00 |
| Rn7sk | 199.48 | 1.54 | 0.00 |
| Gm11266 | 38.55 | 1.06 | 0.00 |
| ENSMUSG00000130839 | 10.88 | 1.18 | 0.00 |
| Cd83 | 83.20 | 1.13 | 0.00 |
| ENSMUSG00000121483 | 27.23 | 1.15 | 0.00 |
| Rps13-ps2 | 21.74 | -2.87 | 0.00 |
| Gm12191 | 12.12 | -4.12 | 0.00 |
| Lpar2 | 21.24 | -1.43 | 0.00 |
| Rpl9-ps6 | 185.94 | -1.45 | 0.00 |
| Tcea1-ps1 | 12.53 | -1.26 | 0.00 |
| Ndufb4b | 108.41 | 1.77 | 0.00 |
| Btf3l4b | 25.24 | -1.55 | 0.00 |
| Gm10052 | 12.79 | -1.58 | 0.00 |
| Gm49518 | 11.75 | 1.44 | 0.00 |
| Gm15890 | 37.52 | 1.01 | 0.00 |
| Gm12669 | 24.92 | -1.14 | 0.00 |
| Isyna1 | 86.77 | -1.14 | 0.00 |
| mt-Atp8 | 9801.93 | 1.55 | 0.00 |
| Gm3724 | 5.21 | -1.65 | 0.00 |
| Ube2n-ps1 | 5.08 | -2.61 | 0.00 |
| ENSMUSG00000122459 | 31.76 | 1.25 | 0.00 |
| Rpl37rt | 21.92 | -4.22 | 0.00 |
| Bhmt-ps1 | 48.28 | -1.35 | 0.00 |
| Rps7-ps3 | 54.83 | -2.72 | 0.00 |
| Cd276 | 39.82 | -1.44 | 0.00 |
| P2ry10b | 19.13 | 1.10 | 0.00 |
| Gm16098 | 27.84 | 1.26 | 0.00 |
| Cldn7 | 9.09 | 1.19 | 0.00 |
| Gm10157 | 25.10 | -1.20 | 0.00 |
| ENSMUSG00000141552 | 13.85 | 1.10 | 0.00 |
| Spdya | 14.28 | 1.12 | 0.00 |
| Nutf2-ps1 | 18.49 | -1.32 | 0.00 |
| Gm6477 | 9.58 | -1.59 | 0.00 |
| ENSMUSG00000138427 | 84.83 | -2.84 | 0.00 |
| Arg2 | 11.81 | 1.28 | 0.00 |
| Gm29216 | 7900.22 | -2.54 | 0.00 |
| Gm5526 | 11.40 | -3.82 | 0.00 |
| Ms4a6b | 58.12 | 1.01 | 0.00 |
| Dpy19l3 | 159.02 | -2.12 | 0.00 |
| ENSMUSG00000134769 | 28.13 | 1.45 | 0.00 |
| Ihh | 30.63 | -2.25 | 0.01 |
| Saa1 | 1967.87 | -2.16 | 0.01 |
| Gm57587 | 9.64 | 1.09 | 0.01 |
| Gm21974 | 11.66 | -1.92 | 0.01 |
| Mmp7 | 13.34 | 1.82 | 0.01 |
| Gm10222 | 6611.33 | 1.79 | 0.01 |
| Gm49190 | 37.10 | -1.14 | 0.01 |
| Gm33543 | 308.55 | 1.07 | 0.01 |
| Idi1-ps2 | 29.11 | 1.09 | 0.01 |
| Zfp1008 | 9.59 | 1.22 | 0.01 |
| Gm9824 | 12.36 | -1.37 | 0.01 |
| ENSMUSG00000129906 | 37.01 | -2.48 | 0.01 |
| Rab7-ps1 | 9.67 | -1.35 | 0.01 |
| Gm4735 | 44.77 | -3.99 | 0.01 |
| Gm10095 | 16.23 | -1.20 | 0.01 |
| Klrb1c | 18.98 | 1.00 | 0.01 |
| Gm14121 | 3.52 | -1.87 | 0.01 |
| ENSMUSG00000127021 | 4.50 | 1.38 | 0.01 |
| Gm9761 | 14.38 | -1.16 | 0.01 |
| Hmgb1-ps3 | 5.58 | 2.55 | 0.01 |
| Hcn2 | 7.64 | -1.52 | 0.01 |
| Gm28706 | 19.94 | 1.05 | 0.01 |
| Ifitm6 | 11.85 | 1.20 | 0.01 |
| Gm12522 | 16.44 | -2.71 | 0.01 |
| Gm56696 | 5.78 | 1.40 | 0.01 |
| Ankrd9 | 31.04 | -1.04 | 0.01 |
| Gm47544 | 46.69 | -1.35 | 0.01 |
| ENSMUSG00000140389 | 6.64 | 1.06 | 0.01 |
6.1.1.2 Males only
There are 279 significantly differentially expressed genes (FDR < 0.01, |log2FC| > 1) in the liver between Cre-AAV and GFP control switch mice.
Diagnostic plots for the DE analysis
- A histogram enriched for low p-values shows the presence of true differential expression (deviation from the uniform null), rather than an all-noise result.
- The log(baseMean) distribution for significant genes being skewed toward moderate–high counts indicates findings are driven by well-expressed features, not low-count noise that can inflate fold-changes and p-values.
Significantly differentially expressed genes in liver
Cre-AAV and GFP control
(FDR < 0.01, |log2FC| > 1)
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Rn7s1 | 830.76 | 2.39 | 0.00 |
| Gm12481 | 45.12 | -8.87 | 0.00 |
| Gm22009 | 29.41 | 3.65 | 0.00 |
| Gm10076 | 1286.01 | 1.35 | 0.00 |
| Rpl35a-ps6 | 41.21 | -21.68 | 0.00 |
| Rpl35a | 3531.67 | 1.04 | 0.00 |
| Ulk1 | 1029.37 | -1.06 | 0.00 |
| Dll1 | 39.41 | -1.37 | 0.00 |
| Gm15387 | 14.61 | -7.24 | 0.00 |
| mt-Nd6 | 24270.23 | 1.30 | 0.00 |
| Vcp-rs | 55.47 | -2.88 | 0.00 |
| Sipa1l3 | 84.90 | -1.16 | 0.00 |
| Gm8566 | 77.66 | -3.20 | 0.00 |
| Abca2 | 568.48 | -1.54 | 0.00 |
| Apoc2l | 454.65 | 1.04 | 0.00 |
| Rpl18-ps2 | 21.59 | -4.65 | 0.00 |
| Ndufb1 | 899.87 | 1.07 | 0.00 |
| Fgfr4 | 482.85 | -1.00 | 0.00 |
| Lrp1 | 8088.56 | -1.17 | 0.00 |
| Gstm2-ps1 | 48.05 | -3.53 | 0.00 |
| Tenm3 | 311.48 | -1.01 | 0.00 |
| Ptprf | 2390.07 | -1.20 | 0.00 |
| Gm45855 | 26.12 | -2.74 | 0.00 |
| Slco2a1 | 801.63 | -1.18 | 0.00 |
| Mov10 | 223.14 | -1.31 | 0.00 |
| Gm10263 | 12.62 | -5.89 | 0.00 |
| Gm10073 | 25.25 | -3.56 | 0.00 |
| Rn7sk | 180.23 | 2.01 | 0.00 |
| ENSMUSG00000143433 | 24.43 | -4.19 | 0.00 |
| Kcp | 60.71 | -1.75 | 0.00 |
| Slc26a1 | 2306.99 | -1.12 | 0.00 |
| Gm28437 | 84421.94 | 1.22 | 0.00 |
| Gm4332 | 26.92 | -3.57 | 0.00 |
| Eef2-ps2 | 21.89 | -3.87 | 0.00 |
| Ttyh3 | 146.91 | -1.02 | 0.00 |
| Tmppe | 29.09 | -1.47 | 0.00 |
| Rpl28-ps1 | 42.52 | -2.87 | 0.00 |
| Llph-ps2 | 153.57 | 1.24 | 0.00 |
| Glns-ps1 | 22.44 | -3.80 | 0.00 |
| Gm44787 | 64.41 | 1.29 | 0.00 |
| mt-Rnr2 | 26254.02 | 1.31 | 0.00 |
| Wdr6 | 225.77 | -1.20 | 0.00 |
| Gm11478 | 37.33 | -3.15 | 0.00 |
| mt-Ts1 | 8.67 | -6.48 | 0.00 |
| Sult1d1 | 7050.73 | 1.23 | 0.00 |
| Gm4149 | 26.70 | -3.47 | 0.00 |
| Mmp15 | 568.82 | -1.31 | 0.00 |
| Glg1 | 618.07 | -1.06 | 0.00 |
| Gm8730 | 38.62 | -3.12 | 0.00 |
| Ntn3 | 86.17 | -1.14 | 0.00 |
| mt-Nd5 | 112471.87 | 1.05 | 0.00 |
| Prrc2b | 786.02 | -1.08 | 0.00 |
| Gm16437 | 12.77 | -3.73 | 0.00 |
| Got2-ps1 | 50.37 | -1.79 | 0.00 |
| Gm4366 | 45.90 | -2.24 | 0.00 |
| Rps13-ps2 | 17.78 | -4.34 | 0.00 |
| Gem | 73.48 | 1.06 | 0.00 |
| Bnip3 | 9057.70 | 1.03 | 0.00 |
| Gm10221 | 28.96 | -2.94 | 0.00 |
| ENSMUSG00000140457 | 645.51 | 1.08 | 0.00 |
| Glo1-ps | 38.32 | -2.76 | 0.00 |
| Gm6204 | 27.29 | -3.58 | 0.00 |
| Gm13611 | 10.64 | -5.57 | 0.00 |
| Zfp931 | 151.31 | 1.12 | 0.00 |
| Rps16-ps2 | 60.07 | -2.69 | 0.00 |
| Gm12174 | 18.93 | -2.94 | 0.00 |
| ENSMUSG00000128633 | 69.82 | -3.56 | 0.00 |
| Cox5b-ps | 30.67 | -2.53 | 0.00 |
| ENSMUSG00000135866 | 197.29 | -3.57 | 0.00 |
| Gabbr2 | 251.86 | -1.54 | 0.00 |
| Gm15163 | 32.17 | -2.59 | 0.00 |
| ENSMUSG00000137224 | 104.65 | -1.90 | 0.00 |
| Tpi-rs11 | 5.57 | -5.23 | 0.00 |
| Gm28661 | 121201.09 | 1.03 | 0.00 |
| Foxq1 | 122.17 | -1.44 | 0.00 |
| Pgam1-ps2 | 21.91 | -2.94 | 0.00 |
| Ms4a6b | 37.59 | 1.51 | 0.00 |
| Mknk2 | 1424.28 | -1.02 | 0.00 |
| Akap17a | 172.66 | -1.16 | 0.00 |
| Gm6548 | 68.88 | -1.12 | 0.00 |
| Fn1 | 17956.83 | -1.21 | 0.00 |
| Ap2m1-ps | 47.51 | -2.03 | 0.00 |
| Nup210 | 220.88 | -1.14 | 0.00 |
| Zbtb42 | 88.86 | -1.10 | 0.00 |
| ENSMUSG00000135935 | 9.62 | 4.09 | 0.00 |
| Gstp-ps | 180.07 | -3.04 | 0.00 |
| Gm5805 | 9.69 | -3.89 | 0.00 |
| Gm9816 | 15.44 | -2.76 | 0.00 |
| Gm44170 | 57.00 | -1.83 | 0.00 |
| Zfp85 | 59.08 | 1.01 | 0.00 |
| Gm14586 | 30.77 | -2.86 | 0.00 |
| Gm13436 | 25.88 | -3.28 | 0.00 |
| Clec7a | 204.54 | 1.06 | 0.00 |
| ENSMUSG00000126438 | 12.18 | -3.20 | 0.00 |
| Gm45774 | 19.92 | 2.48 | 0.00 |
| Gm7600 | 12.26 | -4.49 | 0.00 |
| Nphs1 | 4.55 | 3.81 | 0.00 |
| Abca3 | 921.23 | -1.04 | 0.00 |
| Lars2 | 40213.28 | 1.19 | 0.00 |
| Uba52rt | 168.94 | -1.73 | 0.00 |
| Gm9616 | 12.20 | -3.39 | 0.00 |
| Mfhas1 | 317.75 | -1.18 | 0.00 |
| Gm37035 | 168.67 | -1.06 | 0.00 |
| Gm9755 | 18.05 | -2.55 | 0.00 |
| Rpl23a-ps3 | 23.48 | -2.51 | 0.00 |
| 2010001A14Rik | 131.74 | 1.01 | 0.00 |
| Gm9625 | 25.61 | -2.37 | 0.00 |
| Gm6344 | 12.16 | -2.83 | 0.00 |
| Gm10039 | 16.61 | -2.85 | 0.00 |
| Gm6652 | 235.21 | -1.45 | 0.00 |
| Igsf8 | 113.92 | -1.10 | 0.00 |
| Eif4a-ps4 | 79.49 | -1.59 | 0.00 |
| Rps3a2 | 57.75 | -1.99 | 0.00 |
| ENSMUSG00000130597 | 7.91 | 3.14 | 0.00 |
| Ccdc148 | 51.30 | 1.06 | 0.00 |
| Gm7536 | 93.43 | -1.82 | 0.00 |
| Sort1 | 257.10 | -1.30 | 0.00 |
| Gm6733 | 14.45 | -2.93 | 0.00 |
| Gm12918 | 62.28 | -1.98 | 0.00 |
| Cxcl2 | 7.09 | 2.47 | 0.00 |
| ENSMUSG00000126686 | 56.16 | 1.20 | 0.00 |
| Farp1 | 250.46 | -1.02 | 0.00 |
| ENSMUSG00000132604 | 16.21 | -3.19 | 0.00 |
| Sap18b | 31.12 | -1.94 | 0.00 |
| ENSMUSG00000128869 | 7.74 | -5.19 | 0.00 |
| Rpl15-ps3 | 34.21 | -5.43 | 0.00 |
| Agbl3 | 115.30 | 1.08 | 0.00 |
| Rps18-ps6 | 51.75 | -2.31 | 0.00 |
| Cadm4 | 220.38 | -1.09 | 0.00 |
| Rpl19-ps11 | 82.22 | -1.92 | 0.00 |
| Cspg5 | 32.16 | -2.10 | 0.00 |
| Rpl34-ps1 | 50.78 | -4.66 | 0.00 |
| Rps25-ps1 | 12.44 | -3.11 | 0.00 |
| Gm10874 | 18.42 | -2.55 | 0.00 |
| ENSMUSG00000123794 | 24.12 | -1.36 | 0.00 |
| Kif26b | 17.55 | -1.68 | 0.00 |
| ENSMUSG00000143494 | 36.29 | 1.41 | 0.00 |
| Rpsa-ps10 | 70.29 | -1.99 | 0.00 |
| Gm9794 | 60.24 | -2.05 | 0.00 |
| Rps18-ps5 | 34.58 | -3.70 | 0.00 |
| 2810001A02Rik | 158.86 | 1.02 | 0.00 |
| Rps26-ps1 | 15.04 | -7.28 | 0.00 |
| Gm5835 | 22.83 | -2.65 | 0.00 |
| Gm5456 | 13.70 | -4.03 | 0.00 |
| Pzp | 54053.75 | -1.18 | 0.00 |
| Gm11844 | 271.37 | 1.10 | 0.00 |
| Gm57048 | 107.61 | 1.08 | 0.00 |
| Glud-ps | 28.87 | -2.15 | 0.00 |
| Rpl6l | 18.42 | -2.23 | 0.00 |
| Gm5540 | 27.95 | -2.41 | 0.00 |
| Serpinb6b | 83.41 | 1.04 | 0.00 |
| Zfp97 | 134.90 | 1.03 | 0.00 |
| 4921516A02Rik | 58.14 | -1.80 | 0.00 |
| 5033403H07Rik | 575.81 | 1.03 | 0.00 |
| Lpar2 | 23.40 | -1.88 | 0.00 |
| Gm12183 | 21.22 | -2.55 | 0.00 |
| Gm12350 | 25.63 | -2.43 | 0.00 |
| Arhgef16 | 42.71 | -1.27 | 0.00 |
| Rpl7-ps7 | 7.91 | -2.41 | 0.00 |
| Rps23-ps1 | 41.76 | -2.14 | 0.00 |
| Gm379 | 21.93 | -4.38 | 0.00 |
| Nhsl3 | 933.22 | -1.06 | 0.00 |
| Rtl8a | 70.46 | -1.22 | 0.00 |
| Tpm3-rs7 | 16.20 | -2.22 | 0.00 |
| Slc38a3 | 16620.44 | -1.34 | 0.00 |
| Wfdc17 | 299.80 | 1.15 | 0.00 |
| Atp6v0c-ps2 | 7.13 | -2.96 | 0.00 |
| Gm7336 | 334.35 | -1.05 | 0.00 |
| Gm7049 | 12.00 | -2.80 | 0.00 |
| Hspe1-rs1 | 30.45 | -2.23 | 0.00 |
| ENSMUSG00000121793 | 83.33 | -2.50 | 0.00 |
| Gm16573 | 440.88 | 1.27 | 0.00 |
| Ihh | 42.91 | -2.33 | 0.00 |
| Nat1 | 49.55 | 1.01 | 0.00 |
| Gm10232 | 11.41 | -2.67 | 0.00 |
| 4930524O07Rik | 25.51 | 1.17 | 0.00 |
| Gm31583 | 1705.41 | 1.10 | 0.00 |
| Ndufb4c | 248.05 | 1.05 | 0.00 |
| Wnk4 | 33.64 | -1.18 | 0.00 |
| Gm6180 | 5.82 | -3.38 | 0.00 |
| ENSMUSG00000121505 | 192.41 | 1.49 | 0.00 |
| 1700085D22Rik | 24.07 | 1.02 | 0.00 |
| ENSMUSG00000121863 | 146.26 | 1.16 | 0.00 |
| Gm30784 | 212.29 | 1.17 | 0.00 |
| Rpl17-ps3 | 37.90 | -2.01 | 0.00 |
| Gm32281 | 84.20 | 1.47 | 0.00 |
| Gm15889 | 39.60 | 1.29 | 0.00 |
| Rps19-ps6 | 31.72 | -2.46 | 0.00 |
| Cd276 | 47.14 | -1.90 | 0.00 |
| Gm5421 | 6.53 | -3.65 | 0.00 |
| Gm45507 | 152.92 | 1.34 | 0.00 |
| Lnx1 | 12.40 | -3.07 | 0.00 |
| ENSMUSG00000121776 | 34.08 | -2.24 | 0.00 |
| Susd4 | 769.22 | -1.01 | 0.00 |
| ENSMUSG00000122459 | 27.81 | 1.60 | 0.00 |
| Gm49190 | 36.83 | -1.14 | 0.00 |
| BC028528 | 23.92 | 1.27 | 0.00 |
| Gm11964 | 8.74 | -3.49 | 0.00 |
| Cxcl14 | 48.69 | -1.22 | 0.00 |
| Gm5424 | 812.64 | -2.00 | 0.00 |
| Gm15772 | 21.29 | -2.46 | 0.00 |
| Gm6206 | 12.64 | -2.39 | 0.00 |
| Rpl14-ps1 | 43.81 | -1.94 | 0.00 |
| Faap100 | 79.58 | -1.01 | 0.00 |
| Rplp2-ps1 | 23.44 | -2.93 | 0.00 |
| Gm7666 | 33.37 | -2.12 | 0.00 |
| Rps15-ps2 | 6.33 | -3.94 | 0.00 |
| ENSMUSG00000135161 | 90.94 | 1.29 | 0.00 |
| Gm5905 | 21.69 | -2.01 | 0.00 |
| Slc13a3 | 297.39 | -1.35 | 0.00 |
| Klf13 | 755.08 | -1.10 | 0.00 |
| Ftl1-ps1 | 415.27 | -2.03 | 0.00 |
| Gm10250 | 33.40 | -2.18 | 0.00 |
| Gm7730 | 9.25 | -3.39 | 0.01 |
| Gm8355 | 32.41 | -1.65 | 0.01 |
| Gm5422 | 11.10 | -3.03 | 0.01 |
| Gm8399 | 4.91 | -3.85 | 0.01 |
| Cyp1b1 | 17.02 | 1.08 | 0.01 |
| Rpl36a-ps2 | 16.07 | -2.15 | 0.01 |
| Gm56543 | 25.67 | 1.21 | 0.01 |
| Kpna2rt | 15.04 | -2.30 | 0.01 |
| Rab11b-ps2 | 4.40 | -4.42 | 0.01 |
| Casp1 | 48.41 | 1.05 | 0.01 |
| Gm2962 | 10.49 | -2.66 | 0.01 |
| Rpl35rt | 92.16 | -2.56 | 0.01 |
| 2810013P06Rik | 155.27 | 1.05 | 0.01 |
| Rpl31-ps8 | 32.16 | -1.77 | 0.01 |
| Ndufb4b | 87.04 | 2.65 | 0.01 |
| Smpd3 | 37.41 | -1.71 | 0.01 |
| ENSMUSG00000132147 | 46.32 | -2.08 | 0.01 |
| Gm10778 | 67.40 | 1.01 | 0.01 |
| Arg2 | 7.33 | 1.85 | 0.01 |
| Rpsa-ps2 | 7.33 | -3.50 | 0.01 |
| Mug2 | 7390.61 | -1.10 | 0.01 |
| Eno1b | 29.58 | -3.36 | 0.01 |
| ENSMUSG00000125136 | 5.87 | -2.78 | 0.01 |
| Ccdc152 | 3315.21 | 1.00 | 0.01 |
| Rps27a-ps2 | 42.09 | -1.65 | 0.01 |
| Gm20056 | 9.93 | -2.31 | 0.01 |
| ENSMUSG00000139771 | 115.89 | -2.34 | 0.01 |
| Gm7816 | 20.63 | -2.02 | 0.01 |
| Cyp2c23 | 3904.20 | -1.19 | 0.01 |
| Jchain | 93.33 | 1.14 | 0.01 |
| Srebf1 | 1786.93 | -2.59 | 0.01 |
| Hspd1-ps3 | 48.06 | -1.61 | 0.01 |
| Sdk2 | 7.97 | -1.92 | 0.01 |
| Chrna4 | 8.34 | -4.71 | 0.01 |
| Gm21399 | 46.08 | -1.81 | 0.01 |
| Pdxk | 799.12 | -1.20 | 0.01 |
| Mif-ps4 | 6.85 | -3.94 | 0.01 |
| Gm5182 | 8.95 | -3.01 | 0.01 |
| Adrm1b | 29.01 | -2.30 | 0.01 |
| Gm12744 | 340.15 | -1.00 | 0.01 |
| Cobl | 240.61 | -1.31 | 0.01 |
| Rps10-ps1 | 10.28 | -3.22 | 0.01 |
| ENSMUSG00000132047 | 11.93 | 1.66 | 0.01 |
| Gm4294 | 11.09 | 2.68 | 0.01 |
| ENSMUSG00000128448 | 28.82 | 1.23 | 0.01 |
| Il1b | 67.35 | 1.43 | 0.01 |
| Gm30938 | 28.19 | 1.03 | 0.01 |
| Col1a1 | 49.78 | -1.25 | 0.01 |
| Gm56749 | 211.90 | 1.02 | 0.01 |
| Klrb1c | 11.80 | 1.59 | 0.01 |
| Gm4459 | 10.44 | -2.91 | 0.01 |
| Dclk3 | 91.43 | -1.43 | 0.01 |
| Syt1 | 194.29 | -1.41 | 0.01 |
| Col15a1 | 65.40 | -1.36 | 0.01 |
| Dpy19l3 | 226.63 | -2.21 | 0.01 |
| Osgin1 | 1011.34 | -1.19 | 0.01 |
| Eef2k | 120.28 | -1.27 | 0.01 |
| Gm7204 | 15.80 | -2.04 | 0.01 |
| ENSMUSG00000121608 | 16.68 | -1.52 | 0.01 |
| Gm35035 | 16.14 | 1.20 | 0.01 |
| Gm57504 | 12.84 | -1.80 | 0.01 |
| Gm6863 | 46.39 | -1.50 | 0.01 |
| Cd83 | 47.24 | 1.10 | 0.01 |
| Gm10053 | 80.81 | -2.25 | 0.01 |
| Gm6170 | 9.82 | -2.95 | 0.01 |
| Gm10288 | 85.93 | -2.21 | 0.01 |
6.1.1.3 Females only
There are 271 significantly differentially expressed genes (FDR < 0.01, |log2FC| > 1) in the liver between female Cre-AAV and GFP control switch mice.
Diagnostic plots for the DE analysis
- A histogram enriched for low p-values shows the presence of true differential expression (deviation from the uniform null), rather than an all-noise result.
- The log(baseMean) distribution for significant genes being skewed toward moderate–high counts indicates findings are driven by well-expressed features, not low-count noise that can inflate fold-changes and p-values.
Significantly differentially expressed genes in liver
Cre-AAV and GFP control
(FDR < 0.01, |log2FC| > 1)
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Gstm2-ps1 | 56.95 | -4.18 | 0.00 |
| Ftl1-ps1 | 616.64 | -2.90 | 0.00 |
| ENSMUSG00000121793 | 134.00 | -3.25 | 0.00 |
| Gm13436 | 37.30 | -4.58 | 0.00 |
| Oaz1-ps | 167.06 | -2.71 | 0.00 |
| Gm8730 | 65.75 | -3.92 | 0.00 |
| Gm10163 | 44.25 | -2.82 | 0.00 |
| Gm5540 | 37.08 | -3.89 | 0.00 |
| Rpl35rt | 153.90 | -2.97 | 0.00 |
| Gm14586 | 58.66 | -3.71 | 0.00 |
| Gm5452 | 36.99 | -3.56 | 0.00 |
| Rpl18-ps2 | 38.76 | -3.75 | 0.00 |
| Rpl17-ps3 | 81.42 | -3.34 | 0.00 |
| Gm11478 | 64.04 | -3.59 | 0.00 |
| Gm15427 | 104.00 | -3.09 | 0.00 |
| Gm10073 | 43.41 | -4.19 | 0.00 |
| Fmo3 | 6276.21 | 1.31 | 0.00 |
| Gm10263 | 23.25 | -5.46 | 0.00 |
| Rpl34-ps1 | 49.54 | -3.91 | 0.00 |
| Mir6236 | 23.16 | -2.93 | 0.00 |
| Gm4332 | 46.87 | -3.96 | 0.00 |
| Rps19-ps6 | 53.97 | -3.34 | 0.00 |
| Tpt1-ps3 | 189.25 | -2.44 | 0.00 |
| Gm8355 | 57.90 | -2.76 | 0.00 |
| Gm9794 | 87.32 | -2.73 | 0.00 |
| Rps23-ps1 | 72.36 | -2.55 | 0.00 |
| Rps16-ps2 | 100.17 | -2.94 | 0.00 |
| ENSMUSG00000143433 | 31.98 | -3.71 | 0.00 |
| Gm9385 | 67.23 | -2.86 | 0.00 |
| Adrm1b | 43.96 | -3.17 | 0.00 |
| Gm37273 | 37.17 | 2.03 | 0.00 |
| Gm12350 | 43.51 | -3.34 | 0.00 |
| Gm4366 | 69.10 | -2.52 | 0.00 |
| Gm10232 | 20.55 | -3.80 | 0.00 |
| Glns-ps1 | 36.25 | -3.29 | 0.00 |
| Hadhb-ps | 198.94 | -2.09 | 0.00 |
| Gm10221 | 48.86 | -3.16 | 0.00 |
| Gm45855 | 37.81 | -2.83 | 0.00 |
| Rpl28-ps1 | 75.11 | -3.24 | 0.00 |
| Rps6-ps4 | 180.62 | -1.98 | 0.00 |
| Gm15163 | 45.00 | -2.93 | 0.00 |
| Rpl19-ps11 | 142.75 | -2.47 | 0.00 |
| ENSMUSG00000131289 | 23.67 | -3.37 | 0.00 |
| Eif3j2 | 74.10 | -2.31 | 0.00 |
| Gm6863 | 89.31 | -2.30 | 0.00 |
| Hspe1-rs1 | 46.65 | -3.01 | 0.00 |
| Gm6548 | 95.94 | -1.41 | 0.00 |
| Gm21399 | 69.32 | -2.40 | 0.00 |
| Gm9826 | 188.18 | -2.47 | 0.00 |
| Gm7658 | 17.91 | -3.44 | 0.00 |
| Gm7049 | 25.55 | -3.29 | 0.00 |
| Hspb1 | 512.58 | -1.63 | 0.00 |
| Gstp-ps | 26.40 | -3.63 | 0.00 |
| Glo1-ps | 47.48 | -2.77 | 0.00 |
| Rpsa-ps10 | 100.33 | -2.63 | 0.00 |
| Gm7536 | 145.67 | -2.44 | 0.00 |
| Gm6789 | 131.70 | -1.96 | 0.00 |
| Gm44442 | 385.21 | -1.78 | 0.00 |
| Rps3a2 | 99.47 | -2.63 | 0.00 |
| Cd36 | 5420.42 | -1.48 | 0.00 |
| ENSMUSG00000121777 | 752.26 | -1.78 | 0.00 |
| Gm5422 | 15.87 | -4.04 | 0.00 |
| Rps10-ps1 | 23.45 | -4.55 | 0.00 |
| Mif-ps4 | 12.40 | -5.92 | 0.00 |
| Gm10250 | 58.21 | -2.92 | 0.00 |
| Gm7600 | 21.70 | -3.30 | 0.00 |
| Gm10288 | 146.38 | -3.17 | 0.00 |
| Gm4459 | 20.19 | -3.78 | 0.00 |
| Mpv17l | 486.85 | 1.06 | 0.00 |
| Gm5560 | 27.77 | -2.85 | 0.00 |
| Gm9625 | 29.60 | -3.04 | 0.00 |
| Gm16439 | 47.51 | -2.76 | 0.00 |
| Gm9816 | 16.50 | -3.41 | 0.00 |
| Gm8566 | 142.36 | -3.46 | 0.00 |
| Gm12251 | 19.57 | -3.25 | 0.00 |
| Eef2-ps2 | 29.18 | -3.68 | 0.00 |
| Gm2962 | 12.40 | -3.62 | 0.00 |
| Rps18-ps3 | 29.37 | -3.66 | 0.00 |
| Gm4149 | 43.56 | -2.95 | 0.00 |
| Rpl9-ps4 | 28.55 | -2.77 | 0.00 |
| Gm5835 | 29.22 | -2.71 | 0.00 |
| Rps24-ps3 | 46.03 | -2.80 | 0.00 |
| Gm9755 | 22.56 | -3.60 | 0.00 |
| Gpi-ps | 21.72 | -3.29 | 0.00 |
| ENSMUSG00000135866 | 314.47 | -4.00 | 0.00 |
| Ccdc148 | 100.86 | 1.27 | 0.00 |
| Gm12174 | 36.76 | -2.96 | 0.00 |
| Hspd1-ps3 | 66.43 | -2.11 | 0.00 |
| Gm5805 | 19.10 | -4.39 | 0.00 |
| Gm13680 | 20.13 | -2.98 | 0.00 |
| Rpl23a-ps3 | 45.95 | -2.71 | 0.00 |
| Gm13461 | 17.26 | -3.21 | 0.00 |
| Gm16437 | 16.83 | -3.74 | 0.00 |
| Gm5456 | 18.07 | -3.47 | 0.00 |
| Uba52rt | 236.73 | -1.95 | 0.00 |
| Rpl7-ps7 | 19.25 | -2.92 | 0.00 |
| Rps18-ps5 | 56.92 | -4.10 | 0.00 |
| Gm13611 | 14.75 | -5.33 | 0.00 |
| Rps13-ps1 | 47.05 | -2.84 | 0.00 |
| Gm10819 | 10.99 | -3.91 | 0.00 |
| Glud-ps | 47.34 | -2.63 | 0.00 |
| Gm6652 | 306.73 | -1.52 | 0.00 |
| Vcp-rs | 71.89 | -3.61 | 0.00 |
| Rps27a-ps2 | 69.59 | -2.00 | 0.00 |
| Gm15772 | 31.91 | -2.95 | 0.00 |
| Gm10252 | 13731.24 | 1.35 | 0.00 |
| Gm32202 | 39.44 | 1.89 | 0.00 |
| mt-Ts1 | 7.22 | -6.66 | 0.00 |
| Cox5b-ps | 43.28 | -2.69 | 0.00 |
| ENSMUSG00000139771 | 234.92 | -3.23 | 0.00 |
| Rpl14-ps1 | 66.31 | -1.99 | 0.00 |
| ENSMUSG00000121783 | 636.13 | -1.27 | 0.00 |
| Eno1b | 47.81 | -4.09 | 0.00 |
| Mrpl23-ps1 | 21.13 | -3.21 | 0.00 |
| Gm9493 | 42.99 | -2.52 | 0.00 |
| Gm9892 | 24.38 | -2.20 | 0.00 |
| Gm11964 | 12.28 | -4.43 | 0.00 |
| Gm6170 | 14.82 | -2.97 | 0.00 |
| Gm30505 | 109.57 | 1.24 | 0.00 |
| Gm2223 | 30.06 | -2.31 | 0.00 |
| Gm12346 | 27.63 | -2.76 | 0.00 |
| Gm49909 | 875.96 | 1.01 | 0.00 |
| Slc27a1 | 824.35 | -1.35 | 0.00 |
| Rpl17-ps10 | 95.65 | -2.20 | 0.00 |
| Gm12183 | 28.63 | -2.53 | 0.00 |
| Slc41a2 | 157.56 | -1.29 | 0.00 |
| Slc16a13 | 64.44 | -1.57 | 0.00 |
| Sap18b | 44.77 | -2.37 | 0.00 |
| Got2-ps1 | 65.39 | -1.80 | 0.00 |
| ENSMUSG00000130204 | 55.25 | -1.73 | 0.00 |
| Sult2a6 | 42.55 | -2.41 | 0.00 |
| Btf3-ps1 | 27.18 | -2.25 | 0.00 |
| Eif4a-ps4 | 128.04 | -1.74 | 0.00 |
| Gm10874 | 24.59 | -2.35 | 0.00 |
| Gm7666 | 47.96 | -2.69 | 0.00 |
| Rpl6l | 25.18 | -1.87 | 0.00 |
| Pam16l | 14.01 | -3.09 | 0.00 |
| Rps15-ps2 | 9.63 | -3.75 | 0.00 |
| Wdr89 | 106.60 | -1.44 | 0.00 |
| ENSMUSG00000123407 | 9.84 | -4.03 | 0.00 |
| Gm10039 | 24.72 | -2.56 | 0.00 |
| ENSMUSG00000137224 | 150.92 | -1.45 | 0.00 |
| Rps2-ps10 | 49.08 | -9.44 | 0.00 |
| H2ac19 | 841.06 | -1.47 | 0.00 |
| ENSMUSG00000121784 | 164.41 | -1.53 | 0.00 |
| ENSMUSG00000122915 | 16.17 | -4.17 | 0.00 |
| ENSMUSG00000141422 | 514.55 | -1.11 | 0.00 |
| Gm12992 | 82.45 | -1.48 | 0.00 |
| ENSMUSG00000134769 | 25.99 | 2.55 | 0.00 |
| Rpl31-ps8 | 56.84 | -1.91 | 0.00 |
| Acaa1b | 33296.38 | -1.11 | 0.00 |
| Gm13835 | 107.39 | -1.73 | 0.00 |
| Rpl36-ps12 | 56.57 | -2.09 | 0.00 |
| Vnn1 | 7032.14 | -1.06 | 0.00 |
| Sema5b | 51.77 | -1.38 | 0.00 |
| ENSMUSG00000141528 | 28.43 | -1.88 | 0.00 |
| ENSMUSG00000132147 | 90.49 | -3.00 | 0.00 |
| Actr3-ps | 15.76 | -2.45 | 0.00 |
| Rps10-ps2 | 59.45 | -1.87 | 0.00 |
| Gm6136 | 75.47 | -1.81 | 0.00 |
| Ntn3 | 107.00 | -1.07 | 0.00 |
| Ndufb4c | 333.56 | 1.07 | 0.00 |
| Gm13456 | 618.96 | -2.17 | 0.00 |
| Gm15519 | 13.55 | -3.08 | 0.00 |
| Rps26-ps1 | 22.57 | -8.32 | 0.00 |
| Gm10222 | 7355.03 | 2.47 | 0.00 |
| Rps18-ps6 | 114.18 | -2.95 | 0.00 |
| ENSMUSG00000128633 | 117.00 | -3.16 | 0.00 |
| Tmem238 | 406.11 | -1.14 | 0.00 |
| Map2k6 | 141.58 | 1.55 | 0.00 |
| Gm56542 | 154.02 | 4.69 | 0.00 |
| Gm5436 | 16.98 | -3.18 | 0.00 |
| Rps27rt | 231.43 | -2.31 | 0.00 |
| ENSMUSG00000132256 | 11.62 | -2.95 | 0.00 |
| Gm6055 | 10.53 | -2.85 | 0.00 |
| Gm8203 | 7.28 | -3.74 | 0.00 |
| Gm57204 | 53.81 | 1.36 | 0.00 |
| ENSMUSG00000126438 | 17.29 | -3.18 | 0.00 |
| Scand1 | 349.22 | -1.04 | 0.00 |
| Gm10069 | 37.29 | -1.15 | 0.00 |
| Serpina12 | 101.97 | 1.58 | 0.00 |
| Rps25-ps1 | 19.98 | -3.04 | 0.00 |
| Akap17a | 247.85 | -1.28 | 0.00 |
| Gm6204 | 37.46 | -3.99 | 0.00 |
| Serpina1e | 3916.20 | 3.50 | 0.00 |
| ENSMUSG00000125175 | 27.91 | -2.60 | 0.00 |
| Atp5pb-ps | 42.85 | -1.78 | 0.00 |
| Gm2225 | 12.96 | -2.92 | 0.00 |
| ENSMUSG00000121597 | 26.68 | 7.82 | 0.00 |
| Tmed2b | 24.40 | -1.77 | 0.00 |
| Gm7816 | 24.75 | -2.49 | 0.00 |
| Hspa1b | 174.94 | -1.05 | 0.00 |
| ENSMUSG00000138136 | 353.63 | -1.09 | 0.00 |
| Gm14097 | 593.36 | 1.34 | 0.00 |
| Cyp26b1 | 425.37 | -1.05 | 0.00 |
| AK157302 | 8.20 | -3.33 | 0.00 |
| Gm6733 | 15.17 | -2.53 | 0.00 |
| Gm12918 | 116.30 | -2.78 | 0.00 |
| Gm9616 | 16.44 | -2.70 | 0.00 |
| Fosb | 36.79 | 2.34 | 0.00 |
| Cxcl1 | 101.56 | 1.65 | 0.00 |
| Cirbp | 685.58 | 1.04 | 0.00 |
| Gm10157 | 33.29 | -1.96 | 0.00 |
| Sco2 | 2550.79 | -1.14 | 0.00 |
| Gm20634 | 128.50 | -1.28 | 0.00 |
| Ap2m1-ps | 60.54 | -1.82 | 0.00 |
| Psma5-ps | 25.30 | -2.46 | 0.00 |
| Gm7730 | 11.76 | -3.49 | 0.00 |
| Bhmt1b | 1218.37 | -2.56 | 0.00 |
| Gm29216 | 9425.74 | -3.84 | 0.00 |
| Atp2b2 | 77.71 | -1.61 | 0.00 |
| Gm7204 | 21.60 | -2.07 | 0.00 |
| Gm49077 | 131.11 | 1.46 | 0.00 |
| ENSMUSG00000133704 | 29.41 | -2.15 | 0.00 |
| Gm15542 | 61.77 | -1.27 | 0.00 |
| Upp2 | 4131.01 | 2.22 | 0.00 |
| Gm12669 | 36.97 | -1.58 | 0.00 |
| Gm28661 | 153977.94 | 1.04 | 0.00 |
| Rps15a-ps7 | 19.57 | -2.73 | 0.00 |
| Hmgb1-ps3 | 6.67 | 5.20 | 0.00 |
| Gm12966 | 17.32 | -2.39 | 0.00 |
| Mapk15 | 63.22 | -1.11 | 0.00 |
| Gm10053 | 127.87 | -2.32 | 0.00 |
| Chpf | 87.92 | -1.17 | 0.00 |
| Gm7336 | 414.06 | -1.17 | 0.00 |
| Gm6180 | 8.06 | -3.52 | 0.00 |
| Nudc-ps1 | 7.33 | -3.57 | 0.00 |
| Gm45053 | 31.53 | -1.30 | 0.00 |
| Serinc2 | 251.39 | -1.31 | 0.00 |
| Nrtn | 28.55 | -1.73 | 0.00 |
| Rpl10a-ps1 | 125.72 | -1.32 | 0.00 |
| Pgam1-ps2 | 25.24 | -2.32 | 0.00 |
| Gm2614 | 12.83 | -3.24 | 0.00 |
| Gm6123 | 12.23 | -2.66 | 0.00 |
| mt-Nd5 | 141867.14 | 1.02 | 0.00 |
| Gm5499 | 5.66 | -3.25 | 0.00 |
| Llph-ps2 | 215.84 | 1.00 | 0.01 |
| Etnppl | 2484.41 | 1.02 | 0.01 |
| Rpl9-ps6 | 275.76 | -1.89 | 0.01 |
| Rbm3 | 1912.51 | 1.19 | 0.01 |
| Fam83g | 51.21 | -1.10 | 0.01 |
| Rasl2-9 | 43.90 | 1.05 | 0.01 |
| Gm26608 | 56.34 | 1.07 | 0.01 |
| Gm5182 | 11.42 | -2.61 | 0.01 |
| Gm10095 | 23.09 | -1.68 | 0.01 |
| Gm10036 | 17.84 | -2.56 | 0.01 |
| Kansl2-ps | 7.04 | -2.59 | 0.01 |
| Gm10335 | 57.45 | -1.12 | 0.01 |
| Rab11b-ps2 | 5.19 | -3.92 | 0.01 |
| ENSMUSG00000129688 | 19.14 | -1.79 | 0.01 |
| 2010002M09Rik | 40.36 | 1.04 | 0.01 |
| Scd1 | 21373.27 | 1.24 | 0.01 |
| Tpm3-rs7 | 22.95 | -1.76 | 0.01 |
| Lilrb4b | 118.38 | 1.19 | 0.01 |
| Gm16098 | 36.18 | 1.76 | 0.01 |
| ENSMUSG00000125136 | 10.78 | -2.34 | 0.01 |
| Dmbt1 | 107.15 | 5.92 | 0.01 |
| Rpl3-ps1 | 120.99 | -1.31 | 0.01 |
| Ahcyl | 1584.59 | -1.71 | 0.01 |
| Gm14494 | 16.31 | -2.33 | 0.01 |
| Gm4202 | 8.76 | -2.88 | 0.01 |
| ENSMUSG00000121655 | 26.14 | -2.11 | 0.01 |
| ENSMUSG00000139337 | 94.84 | 1.12 | 0.01 |
| ENSMUSG00000125715 | 38.36 | -1.28 | 0.01 |
| Erdr1y | 232.88 | -1.07 | 0.01 |
| Gm9512 | 21.09 | -2.03 | 0.01 |
| Pdcd5-ps | 16.91 | -1.55 | 0.01 |
| Hectd2 | 84.76 | -1.21 | 0.01 |
| Gm53019 | 30.36 | 1.65 | 0.01 |
| Gm45753 | 8.56 | 3.14 | 0.01 |
| Gm2999 | 11.02 | -2.85 | 0.01 |
6.1.1.4 Common DEGs in males and females
Differential expression analysis comparing Cre-AAV and GFP control groups in liver identified a large number of significantly altered transcripts (FDR < 0.01, |log₂FC| > 1). To focus on robust and biologically relevant signals, we intersected DEGs detected in both male and female mice.
There were 119 common DEGs shared in male and females. The majority corresponded to ribosomal and uncharacterized pseudogenes, reflecting global transcriptional perturbations rather than specific pathway activation.
| gene |
|---|
| Gm16437 |
| Gm9755 |
| Ccdc148 |
| Gm5422 |
| Adrm1b |
| Gm6863 |
| Rpl14-ps1 |
| Rpsa-ps10 |
| Gm8566 |
| Gm7204 |
| Gm5540 |
| Gm6180 |
| Rpl18-ps2 |
| Gm7536 |
| Tpm3-rs7 |
| Rpl28-ps1 |
| Hspd1-ps3 |
| Rps27a-ps2 |
| Gm10053 |
| Eno1b |
| Rps26-ps1 |
| Gm10073 |
| Rps16-ps2 |
| Rps10-ps1 |
| Sap18b |
| Gm5805 |
| Gm15772 |
| Ftl1-ps1 |
| Rps3a2 |
| Gm8730 |
| mt-Ts1 |
| mt-Nd5 |
| Gm13611 |
| Gm12918 |
| Gm10263 |
| Rps25-ps1 |
| Gm7666 |
| Gm10221 |
| Rpl31-ps8 |
| Gm10232 |
| Uba52rt |
| Rpl34-ps1 |
| Gm10250 |
| Rps18-ps6 |
| Gm10288 |
| Rps15-ps2 |
| Gm4149 |
| Glo1-ps |
| Gm10874 |
| Rpl23a-ps3 |
| Rpl35rt |
| Gm7336 |
| Cox5b-ps |
| Gm12174 |
| Got2-ps1 |
| Gm11964 |
| Rpl19-ps11 |
| Ap2m1-ps |
| Pgam1-ps2 |
| Glns-ps1 |
| Gm12183 |
| Eef2-ps2 |
| Gm7816 |
| Vcp-rs |
| Llph-ps2 |
| Ndufb4c |
| Gm14586 |
| Gm4459 |
| Mif-ps4 |
| Gm13436 |
| Gm11478 |
| Gm6733 |
| Gm15163 |
| Gm9816 |
| Gm2962 |
| Rpl6l |
| Gm10039 |
| Gm6548 |
| Gm8355 |
| Gm5456 |
| Gm21399 |
| Gm12350 |
| Rab11b-ps2 |
| Rps19-ps6 |
| Gm9625 |
| Gm6652 |
| Gm6170 |
| Rps23-ps1 |
| Eif4a-ps4 |
| Gm5835 |
| Gm28661 |
| Gstp-ps |
| Gm6204 |
| Gm4332 |
| Rpl7-ps7 |
| Gm9794 |
| Gstm2-ps1 |
| Gm4366 |
| Glud-ps |
| Gm7600 |
| Gm7730 |
| Gm45855 |
| Gm5182 |
| Rps18-ps5 |
| Gm7049 |
| Rpl17-ps3 |
| Gm9616 |
| Ntn3 |
| Hspe1-rs1 |
| Akap17a |
| ENSMUSG00000121793 |
| ENSMUSG00000125136 |
| ENSMUSG00000126438 |
| ENSMUSG00000128633 |
| ENSMUSG00000132147 |
| ENSMUSG00000135866 |
| ENSMUSG00000137224 |
| ENSMUSG00000139771 |
| ENSMUSG00000143433 |
Filtering out pseudogenes, unannotated loci (Gm*), mitochondrial genes, and Ensembl-only identifiers yielded 11 high-confidence nuclear genes consistently dysregulated across sexes, representing the shared hepatic response to Cre-mediated ApoE4→ApoE2 conversion.
Ccdc148, Adrm1b, Tpm3-rs7, Eno1b, Sap18b, Uba52rt, Vcp-rs, Ndufb4c, Ntn3, Hspe1-rs1, Akap17aImportantly, the absence of strong pro-inflammatory or lipid metabolism signatures indicates that the Cre-AAV–driven ApoE4→ApoE2 conversion did not induce overt hepatic stress or metabolic disruption, consistent with physiological tolerance to ApoE2 expression in liver.
6.1.2 Brain
6.1.2.1 All mice (male and females)
There are 369 significantly differentially expressed genes (FDR < 0.01, |log2FC| > 1) in the brain between Cre-AAV and GFP control switch mice.
Diagnostic plots for the DE analysis
- A histogram enriched for low p-values shows the presence of true differential expression (deviation from the uniform null), rather than an all-noise result.
- The log(baseMean) distribution for significant genes being skewed toward moderate–high counts indicates findings are driven by well-expressed features, not low-count noise that can inflate fold-changes and p-values.
Significantly differentially expressed genes in brain
Cre-AAV and GFP control
(FDR < 0.01, |log2FC| > 1)
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Gm4149 | 32.14 | -3.47 | 0.00 |
| Rps6-ps4 | 114.03 | -1.93 | 0.00 |
| Rps13-ps1 | 29.45 | -3.74 | 0.00 |
| Rpl35rt | 127.39 | -3.71 | 0.00 |
| Gm9385 | 44.16 | -3.00 | 0.00 |
| Gm15427 | 62.94 | -3.25 | 0.00 |
| Gm56350 | 25.27 | -23.45 | 0.00 |
| Rps18-ps5 | 21.51 | -4.78 | 0.00 |
| Cox5b-ps | 36.04 | -2.69 | 0.00 |
| Rpl14-ps1 | 54.61 | -2.58 | 0.00 |
| Rpsa-ps10 | 73.01 | -3.03 | 0.00 |
| Rps19-ps6 | 39.57 | -3.65 | 0.00 |
| Gm10288 | 95.03 | -3.25 | 0.00 |
| Gm14586 | 31.34 | -3.37 | 0.00 |
| Gm11478 | 43.13 | -3.64 | 0.00 |
| Gm49388 | 8.17 | -22.20 | 0.00 |
| Rpl17-ps3 | 51.71 | -3.08 | 0.00 |
| Rpl17-ps10 | 78.29 | -2.77 | 0.00 |
| Rps23-ps1 | 47.87 | -2.75 | 0.00 |
| Rpl19-ps11 | 100.00 | -2.77 | 0.00 |
| Gm6560 | 71.28 | -2.25 | 0.00 |
| Rpl28-ps1 | 38.67 | -3.04 | 0.00 |
| Rps24-ps3 | 27.56 | -3.25 | 0.00 |
| ENSMUSG00000121779 | 67.38 | -1.43 | 0.00 |
| Gm8226 | 77.93 | -1.92 | 0.00 |
| Gm10073 | 42.07 | -3.91 | 0.00 |
| Rps16-ps2 | 56.86 | -3.36 | 0.00 |
| Gm15772 | 27.73 | -3.17 | 0.00 |
| Rps3a2 | 68.79 | -2.80 | 0.00 |
| Rpl9-ps6 | 207.66 | -2.48 | 0.00 |
| Rpl34-ps1 | 58.67 | -5.61 | 0.00 |
| ENSMUSG00000143433 | 23.97 | -3.95 | 0.00 |
| Rpl3-ps1 | 177.92 | -1.92 | 0.00 |
| Gm8566 | 19.88 | -3.26 | 0.00 |
| Rpl36a-ps2 | 19.81 | -2.69 | 0.00 |
| Gm7308 | 39.17 | -2.16 | 0.00 |
| ENSMUSG00000121793 | 82.31 | -3.29 | 0.00 |
| Eno1b | 46.82 | -3.11 | 0.00 |
| Fbxl15 | 309.95 | -1.04 | 0.00 |
| Rps27a-ps2 | 47.51 | -2.21 | 0.00 |
| Uba52rt | 146.27 | -2.28 | 0.00 |
| Gm9794 | 53.70 | -2.40 | 0.00 |
| Gm5436 | 13.72 | -3.83 | 0.00 |
| Gm13456 | 185.31 | -2.33 | 0.00 |
| ENSMUSG00000139771 | 140.96 | -3.10 | 0.00 |
| Gm9493 | 32.22 | -2.97 | 0.00 |
| Gm11223 | 39.02 | -2.19 | 0.00 |
| Nme3 | 427.94 | -1.08 | 0.00 |
| Gm6180 | 26.71 | -2.47 | 0.00 |
| Gm10053 | 137.06 | -2.69 | 0.00 |
| Gm6789 | 40.04 | -2.08 | 0.00 |
| ENSMUSG00000128633 | 87.85 | -4.13 | 0.00 |
| ENSMUSG00000137224 | 81.76 | -1.73 | 0.00 |
| Gm4332 | 27.83 | -4.19 | 0.00 |
| Rps10-ps2 | 42.55 | -2.15 | 0.00 |
| Gm10052 | 36.46 | -1.53 | 0.00 |
| Gm22009 | 108.53 | 3.86 | 0.00 |
| Rpl23a-ps3 | 36.22 | -2.72 | 0.00 |
| Gm16437 | 13.55 | -3.08 | 0.00 |
| Nicol1 | 359.05 | -1.16 | 0.00 |
| ENSMUSG00000132604 | 23.26 | -3.53 | 0.00 |
| Gm9816 | 28.68 | -2.67 | 0.00 |
| Gm4366 | 80.72 | -2.31 | 0.00 |
| Gm8730 | 22.80 | -3.64 | 0.00 |
| Gm12254 | 19.52 | -2.37 | 0.00 |
| Nrtn | 70.42 | -1.71 | 0.00 |
| Gm5499 | 26.96 | -2.38 | 0.00 |
| Rpl31-ps8 | 54.28 | -2.07 | 0.00 |
| Gm8203 | 16.15 | -3.22 | 0.00 |
| Rps15a-ps7 | 15.30 | -3.26 | 0.00 |
| ENSMUSG00000121655 | 13.35 | -2.70 | 0.00 |
| ENSMUSG00000121784 | 141.92 | -1.99 | 0.00 |
| Rps25-ps1 | 13.20 | -4.32 | 0.00 |
| Rpl18-ps2 | 19.06 | -3.97 | 0.00 |
| Rpl10a-ps1 | 64.06 | -1.67 | 0.00 |
| Hadhb-ps | 26.49 | -1.66 | 0.00 |
| Gm10250 | 41.82 | -2.47 | 0.00 |
| Nudc-ps1 | 12.44 | -2.73 | 0.00 |
| 1810049J17Rik | 13.52 | -4.30 | 0.00 |
| Gm12892 | 86.68 | -2.36 | 0.00 |
| Gm8355 | 58.54 | -1.68 | 0.00 |
| Gm37035 | 222.55 | -1.13 | 0.00 |
| Pgam1-ps2 | 69.18 | -2.69 | 0.00 |
| Sap18b | 29.87 | -2.23 | 0.00 |
| Gm4202 | 64.78 | -1.76 | 0.00 |
| Gm10221 | 21.69 | -3.22 | 0.00 |
| Gm12918 | 95.27 | -3.02 | 0.00 |
| Rps27rt | 127.14 | -2.80 | 0.00 |
| Gm7536 | 94.72 | -2.57 | 0.00 |
| ENSMUSG00000138427 | 13.96 | -3.59 | 0.00 |
| Gm13611 | 9.98 | -5.73 | 0.00 |
| ENSMUSG00000121777 | 294.76 | -1.79 | 0.00 |
| Gm7600 | 16.41 | -4.28 | 0.00 |
| Aldoart1 | 15.50 | -3.42 | 0.00 |
| Glns-ps1 | 27.12 | -2.70 | 0.00 |
| Oaz1-ps | 63.61 | -2.53 | 0.00 |
| Gm6863 | 46.20 | -2.13 | 0.00 |
| Ube2srt | 20.90 | -2.67 | 0.00 |
| Gm13436 | 23.63 | -4.15 | 0.00 |
| Eef2-ps2 | 16.93 | -3.03 | 0.00 |
| Fam221b | 58.28 | -1.23 | 0.00 |
| Scand1 | 368.57 | -1.11 | 0.00 |
| mt-Co2 | 52612.16 | -1.22 | 0.00 |
| Actr3-ps | 17.91 | -2.37 | 0.00 |
| Atp6v0c-ps2 | 39.07 | -1.97 | 0.00 |
| Gm4459 | 11.08 | -3.21 | 0.00 |
| Gm12346 | 129.10 | -1.35 | 0.00 |
| Ap2m1-ps | 151.10 | -1.31 | 0.00 |
| Ldhb-ps | 44.98 | -2.14 | 0.00 |
| Vcp-rs | 48.51 | -1.74 | 0.00 |
| Rps18-ps6 | 37.62 | -3.38 | 0.00 |
| Rps7-ps3 | 49.39 | -2.96 | 0.00 |
| Gm10263 | 12.83 | -4.54 | 0.00 |
| Pcsk1n | 9530.38 | -1.08 | 0.00 |
| Gm2225 | 13.47 | -3.67 | 0.00 |
| Gm9625 | 22.29 | -1.89 | 0.00 |
| Gm5805 | 13.06 | -4.38 | 0.00 |
| ENSMUSG00000121783 | 439.67 | -1.56 | 0.00 |
| Gm45855 | 12.83 | -3.98 | 0.00 |
| ENSMUSG00000131289 | 12.38 | -2.49 | 0.00 |
| Rpl6l | 20.09 | -2.25 | 0.00 |
| Gm12251 | 11.83 | -3.19 | 0.00 |
| Tmem238 | 65.41 | -1.09 | 0.00 |
| Eif4a-ps4 | 75.56 | -1.52 | 0.00 |
| Gpi-ps | 57.80 | -2.40 | 0.00 |
| Gm7666 | 20.16 | -3.03 | 0.00 |
| Gm6204 | 28.93 | -3.86 | 0.00 |
| H3c15 | 39.97 | -1.23 | 0.00 |
| Gm6136 | 52.82 | -1.72 | 0.00 |
| Gm14150 | 18.33 | -2.84 | 0.00 |
| Gstp-ps | 13.48 | -3.28 | 0.00 |
| Gm12174 | 18.56 | -3.10 | 0.00 |
| Gm14121 | 11.27 | -2.67 | 0.00 |
| Tpt1-ps3 | 57.66 | -2.39 | 0.00 |
| Rps26-ps1 | 14.10 | -7.13 | 0.00 |
| Prkcz2 | 28.87 | -2.16 | 0.00 |
| Hspe1-rs1 | 14.15 | -3.22 | 0.00 |
| Gm8399 | 30.52 | -2.23 | 0.00 |
| Gm10163 | 45.93 | -1.84 | 0.00 |
| Gm2614 | 8.44 | -4.27 | 0.00 |
| 4632415L05Rik | 13.95 | -7.12 | 0.00 |
| Rpl7-ps7 | 6.61 | -3.22 | 0.00 |
| Tmsb10b | 24.99 | -1.64 | 0.00 |
| Rps15-ps2 | 9.70 | -3.34 | 0.00 |
| Mif-ps4 | 10.76 | -4.49 | 0.00 |
| Gm12481 | 40.91 | -6.50 | 0.00 |
| Rps10-ps1 | 12.85 | -4.16 | 0.00 |
| Ftl1-ps1 | 44.16 | -2.55 | 0.00 |
| H2ac19 | 199.63 | -1.47 | 0.00 |
| Yjefn3 | 120.58 | -1.07 | 0.00 |
| Gm12183 | 38.98 | -1.95 | 0.00 |
| Gm3571 | 7.69 | -4.32 | 0.00 |
| Gm2223 | 19.27 | -1.68 | 0.00 |
| Gm37530 | 11.01 | 1.78 | 0.00 |
| Gm5844 | 26.21 | -1.61 | 0.00 |
| Gm6344 | 9.56 | -3.51 | 0.00 |
| Gm2999 | 17.93 | -2.75 | 0.00 |
| Gm10039 | 16.02 | -2.49 | 0.00 |
| Gm5526 | 12.57 | -5.43 | 0.00 |
| Erhrt-ps | 12.10 | -3.12 | 0.00 |
| Gm5421 | 16.50 | -2.26 | 0.00 |
| Gm16439 | 8.40 | -3.03 | 0.00 |
| Gm13461 | 15.16 | -2.46 | 0.00 |
| Rn7s1 | 495.73 | 1.82 | 0.00 |
| Gm5835 | 23.57 | -2.03 | 0.00 |
| Rplp2-ps1 | 21.59 | -4.75 | 0.00 |
| Gm13835 | 42.67 | -1.70 | 0.00 |
| Gm9616 | 13.86 | -2.87 | 0.00 |
| Gm14494 | 12.60 | -2.30 | 0.00 |
| Gm10036 | 12.12 | -3.46 | 0.00 |
| Adrm1b | 18.73 | -2.25 | 0.00 |
| Gm5424 | 12.44 | -2.38 | 0.00 |
| ENSMUSG00000123407 | 4.95 | -4.39 | 0.00 |
| Rpl37rt | 29.84 | -7.02 | 0.00 |
| Gstm2-ps1 | 9.80 | -3.48 | 0.00 |
| Btf3-ps1 | 15.43 | -2.32 | 0.00 |
| Sms-ps | 15.42 | -1.90 | 0.00 |
| Rpl36-ps12 | 24.82 | -2.34 | 0.00 |
| Rab11b-ps2 | 13.30 | -2.63 | 0.00 |
| Rn7sk | 450.20 | 1.57 | 0.00 |
| Gm12350 | 15.50 | -2.78 | 0.00 |
| Gm15519 | 5.84 | -3.34 | 0.00 |
| Atp5pb-ps | 19.77 | -1.93 | 0.00 |
| Tpm3-rs7 | 19.00 | -1.81 | 0.00 |
| Gm37811 | 50.18 | -1.38 | 0.00 |
| ENSMUSG00000132287 | 16.47 | -2.92 | 0.00 |
| ENSMUSG00000123149 | 27.17 | -2.06 | 0.00 |
| Gm45051 | 16.53 | -1.45 | 0.00 |
| Nutf2-ps1 | 32.77 | -1.47 | 0.00 |
| Gm12966 | 17.05 | -1.80 | 0.00 |
| Ube2n-ps1 | 15.71 | -2.43 | 0.00 |
| Gm9531 | 12.99 | -2.19 | 0.00 |
| Rpl9-ps4 | 21.85 | -3.15 | 0.00 |
| Gm13680 | 10.57 | -2.12 | 0.00 |
| Ahcyl | 13.84 | -2.52 | 0.00 |
| Gm10819 | 15.69 | -2.49 | 0.00 |
| Mrpl23-ps1 | 14.76 | -2.90 | 0.00 |
| Gm11964 | 5.62 | -3.98 | 0.00 |
| Gm37899 | 14.98 | 1.90 | 0.00 |
| Cdk2ap1rt | 40.72 | -1.61 | 0.00 |
| Pam16l | 10.68 | -2.71 | 0.00 |
| Ywhaq-ps3 | 30.93 | -1.93 | 0.00 |
| Gm3724 | 12.50 | -2.01 | 0.00 |
| Btf3l4b | 31.53 | -2.28 | 0.00 |
| Kansl2-ps | 10.70 | -2.36 | 0.00 |
| Gm21399 | 6.10 | -2.50 | 0.00 |
| Gm7658 | 9.90 | -2.75 | 0.00 |
| B020010K11Rik | 32.49 | -3.15 | 0.00 |
| Eef1a1-ps1 | 26.19 | -1.44 | 0.00 |
| Kcng3 | 23.69 | 1.18 | 0.00 |
| Impdh2-ps | 9.41 | -2.34 | 0.00 |
| ENSMUSG00000138717 | 17.49 | -2.13 | 0.00 |
| Cdr1 | 106.41 | 1.26 | 0.00 |
| APOE | 44215.72 | 2.47 | 0.00 |
| Tpi-rs11 | 10.88 | -3.50 | 0.00 |
| Gm44442 | 131.88 | -1.55 | 0.00 |
| Gm5422 | 13.67 | -2.32 | 0.00 |
| Gm56991 | 57.98 | -1.35 | 0.00 |
| Oxt | 157.95 | -1.75 | 0.00 |
| Gm9824 | 27.66 | -1.55 | 0.00 |
| Mrip-ps | 12.64 | -1.70 | 0.00 |
| Avp | 257.42 | -1.45 | 0.00 |
| ENSMUSG00000126438 | 6.97 | -3.36 | 0.00 |
| AK157302 | 17.49 | -1.91 | 0.00 |
| Gm5905 | 16.17 | -2.68 | 0.00 |
| 9530059O14Rik | 24.78 | 1.47 | 0.00 |
| Rps13-ps2 | 19.30 | -2.30 | 0.00 |
| Gchfr | 23.10 | -1.48 | 0.00 |
| Gm12669 | 25.23 | -1.35 | 0.00 |
| Gm6170 | 5.19 | -3.97 | 0.00 |
| Gm5560 | 8.77 | -2.53 | 0.00 |
| Psma5-ps | 10.66 | -2.59 | 0.00 |
| Gm15421 | 12.70 | -2.30 | 0.00 |
| ENSMUSG00000137056 | 10.92 | -2.24 | 0.00 |
| Grin2b | 5926.08 | 1.07 | 0.00 |
| Gm21986 | 62.79 | -1.93 | 0.00 |
| Gm49521 | 27.14 | 1.24 | 0.00 |
| Pomc | 154.81 | -2.67 | 0.00 |
| Gm6055 | 10.81 | -2.72 | 0.00 |
| Malat1 | 13736.97 | 1.45 | 0.00 |
| Gm7730 | 4.22 | -4.23 | 0.00 |
| Rpl15-ps3 | 42.98 | -3.78 | 0.00 |
| Gm7816 | 18.63 | -1.65 | 0.00 |
| mt-Ts1 | 6.56 | -3.77 | 0.00 |
| Gm10642 | 38.71 | -1.36 | 0.00 |
| Gm5456 | 3.59 | -4.53 | 0.00 |
| Eif3j2 | 24.77 | -1.62 | 0.00 |
| ENSMUSG00000140944 | 13.05 | -1.97 | 0.00 |
| ENSMUSG00000141748 | 78.11 | -1.52 | 0.00 |
| A730035I17Rik | 31.38 | -1.40 | 0.00 |
| Amn | 100.83 | -1.01 | 0.00 |
| Gm50322 | 18.27 | 1.10 | 0.00 |
| Glo1-ps | 6.45 | -2.76 | 0.00 |
| Gm16105 | 95.52 | 1.04 | 0.00 |
| Gm2962 | 4.92 | -2.61 | 0.00 |
| ENSMUSG00000123314 | 68.66 | -1.09 | 0.00 |
| Tcea1-ps1 | 10.64 | -1.41 | 0.00 |
| Amhr2 | 17.15 | -1.05 | 0.00 |
| ENSMUSG00000125669 | 11.96 | -2.05 | 0.00 |
| Gm6477 | 11.68 | -1.77 | 0.00 |
| Gm42583 | 21.36 | 1.62 | 0.00 |
| Gh | 57.81 | -4.88 | 0.00 |
| Gm14703 | 210.00 | -2.07 | 0.00 |
| Gm10232 | 9.85 | -1.80 | 0.00 |
| ENSMUSG00000132256 | 5.19 | -3.45 | 0.00 |
| ENSMUSG00000127515 | 11.39 | -1.65 | 0.00 |
| ENSMUSG00000128869 | 20.90 | -2.75 | 0.00 |
| Hba-a1 | 291.47 | -1.78 | 0.00 |
| ENSMUSG00000136525 | 45052.78 | 1.65 | 0.00 |
| Gm57848 | 42.57 | 1.03 | 0.00 |
| ENSMUSG00000130204 | 99.69 | -1.42 | 0.00 |
| 1700034P13Rik | 48.86 | 1.23 | 0.00 |
| Gm37345 | 28.47 | 1.02 | 0.00 |
| Gm56769 | 26.66 | -1.46 | 0.00 |
| Gm56901 | 11.42 | 1.25 | 0.00 |
| Kcnmb4os1 | 37.87 | -2.01 | 0.00 |
| Hspd1-ps3 | 17.85 | -1.41 | 0.00 |
| 1600020E01Rik | 193.78 | -1.04 | 0.00 |
| ENSMUSG00000133032 | 10.57 | 1.40 | 0.00 |
| Gm9826 | 2.20 | -3.79 | 0.00 |
| ENSMUSG00000136970 | 26.45 | -1.12 | 0.00 |
| Pabpc1l2b | 14.87 | -5.99 | 0.00 |
| Col6a5 | 12.15 | 1.32 | 0.00 |
| Gm10335 | 52.17 | -1.10 | 0.00 |
| Rpph1 | 21.69 | 1.50 | 0.00 |
| Gm14089 | 47.65 | -2.82 | 0.00 |
| Gm20431 | 96.78 | -5.57 | 0.00 |
| Gm5182 | 16.83 | -1.15 | 0.00 |
| ENSMUSG00000125136 | 20.47 | -1.22 | 0.00 |
| Gm11537 | 18.77 | -1.19 | 0.00 |
| Dhx58os | 15.30 | -1.03 | 0.00 |
| Rpsa-ps2 | 7.29 | -2.32 | 0.00 |
| Hbb-bs | 758.55 | -1.64 | 0.00 |
| Gm11175 | 14.70 | -1.55 | 0.00 |
| S1pr4 | 17.52 | -1.20 | 0.00 |
| Tektip1 | 34.53 | -1.03 | 0.00 |
| Gm9755 | 9.47 | -1.96 | 0.00 |
| Gm9761 | 19.19 | -1.37 | 0.00 |
| Pagr1a | 46.21 | -2.49 | 0.00 |
| Gm43062 | 10.51 | 1.24 | 0.00 |
| ENSMUSG00000121782 | 5.81 | -2.63 | 0.00 |
| Crygn | 5.49 | -1.91 | 0.00 |
| Gm3226 | 13.86 | -1.69 | 0.00 |
| Gm9892 | 17.12 | -1.61 | 0.00 |
| Gm49518 | 5.94 | 1.89 | 0.00 |
| Hspb1 | 196.57 | -1.07 | 0.00 |
| ENSMUSG00000132147 | 10.36 | -2.13 | 0.00 |
| Gm3375 | 14.85 | -1.79 | 0.00 |
| ENSMUSG00000133162 | 13.07 | 1.31 | 0.00 |
| Gm37123 | 6.85 | 1.57 | 0.00 |
| ENSMUSG00000121445 | 18.05 | -1.01 | 0.00 |
| Gm5452 | 5.28 | -2.42 | 0.00 |
| Hba-a2 | 434.02 | -1.56 | 0.00 |
| ENSMUSG00000121644 | 17.04 | -1.32 | 0.00 |
| Mypopos | 13.49 | 1.32 | 0.00 |
| Rn18s-rs5 | 224935.62 | 1.01 | 0.00 |
| ENSMUSG00000129048 | 29.07 | 1.45 | 0.00 |
| Arhgap27os2 | 12.87 | -1.50 | 0.00 |
| Tbxa2r | 17.92 | -1.16 | 0.00 |
| Dnajb6-ps | 10.44 | -1.69 | 0.00 |
| Gm56672 | 25.08 | -2.34 | 0.00 |
| ENSMUSG00000122915 | 11.94 | -2.54 | 0.00 |
| ENSMUSG00000143322 | 41.37 | -1.21 | 0.00 |
| Gm15163 | 3.41 | -2.83 | 0.00 |
| ENSMUSG00000123794 | 23.61 | -1.69 | 0.00 |
| ENSMUSG00000131217 | 22.07 | -1.59 | 0.00 |
| Gm6206 | 19.97 | -1.09 | 0.00 |
| Misp3 | 14.40 | -1.07 | 0.00 |
| ENSMUSG00000138136 | 22.32 | -1.18 | 0.00 |
| Kpna2rt | 7.61 | -2.46 | 0.00 |
| Glud-ps | 9.86 | -1.77 | 0.00 |
| Gm4735 | 47.74 | -3.79 | 0.00 |
| ENSMUSG00000121727 | 11.48 | -3.87 | 0.00 |
| Gm2423 | 22.85 | -1.52 | 0.00 |
| ENSMUSG00000135265 | 23.13 | 2.31 | 0.00 |
| Gm28439 | 538.39 | 1.30 | 0.00 |
| St8sia3os | 13.20 | -1.22 | 0.00 |
| Gm43843 | 35.92 | 1.08 | 0.00 |
| Usp50 | 9.96 | -1.37 | 0.00 |
| Gm6733 | 6.18 | -1.76 | 0.00 |
| Hbb-bt | 117.49 | -1.61 | 0.00 |
| ENSMUSG00000141875 | 22.21 | 1.21 | 0.00 |
| Gm15501 | 20.32 | -3.02 | 0.00 |
| Gm47956 | 12.70 | 1.06 | 0.00 |
| Gm14308 | 112.15 | -1.66 | 0.00 |
| Gm26621 | 10.47 | 1.33 | 0.00 |
| Scp2-ps2 | 6.07 | -2.54 | 0.00 |
| Gm13066 | 16.76 | -3.05 | 0.00 |
| Rps2-ps10 | 10.87 | -6.76 | 0.00 |
| Or7d10 | 10.09 | -1.65 | 0.00 |
| Rps18-ps3 | 5.71 | -2.88 | 0.00 |
| Fev | 8.82 | -1.80 | 0.00 |
| Ltf | 8.03 | -1.94 | 0.00 |
| Calhm6 | 5.37 | -1.46 | 0.00 |
| Gm49378 | 27.78 | 1.83 | 0.00 |
| Bc1 | 6314.60 | -1.45 | 0.01 |
| Gm6682 | 12.08 | -2.08 | 0.01 |
| Tph2 | 247.79 | -1.35 | 0.01 |
| ENSMUSG00000141850 | 7.71 | -1.80 | 0.01 |
| Gm10874 | 12.34 | -1.45 | 0.01 |
| Rab7-ps1 | 12.61 | -1.13 | 0.01 |
| Mir6236 | 17.83 | -1.13 | 0.01 |
| Gm17167 | 44.02 | 2.67 | 0.01 |
| Fam167b | 7.39 | -1.30 | 0.01 |
| Slc6a4 | 114.56 | -1.48 | 0.01 |
| Gm7049 | 6.23 | -2.02 | 0.01 |
| Atp4a | 10.03 | -1.12 | 0.01 |
| ENSMUSG00000130848 | 9.13 | 1.24 | 0.01 |
| Gm9512 | 4.86 | -1.54 | 0.01 |
6.1.2.2 Males only
There are 244 significantly differentially expressed genes (FDR < 0.01, |log2FC| > 1) in the brain between Cre-AAV and GFP control switch mice.
Diagnostic plots for the DE analysis
- A histogram enriched for low p-values shows the presence of true differential expression (deviation from the uniform null), rather than an all-noise result.
- The log(baseMean) distribution for significant genes being skewed toward moderate–high counts indicates findings are driven by well-expressed features, not low-count noise that can inflate fold-changes and p-values.
Significantly differentially expressed genes in brain
Cre-AAV and GFP control
(FDR < 0.01, |log2FC| > 1)
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Gm56350 | 21.63 | -22.39 | 0.00 |
| Gm14089 | 41.39 | -6.09 | 0.00 |
| Rps13-ps1 | 29.93 | -3.77 | 0.00 |
| Rps6-ps4 | 111.46 | -1.91 | 0.00 |
| Gm13436 | 21.56 | -5.40 | 0.00 |
| Rpl14-ps1 | 53.57 | -2.43 | 0.00 |
| Rpl36a-ps2 | 20.29 | -3.18 | 0.00 |
| Gm4149 | 28.38 | -3.65 | 0.00 |
| Gm6180 | 28.51 | -2.81 | 0.00 |
| Rpl23a-ps3 | 38.11 | -2.78 | 0.00 |
| Rpsa-ps10 | 73.52 | -3.15 | 0.00 |
| Gm14586 | 32.11 | -3.36 | 0.00 |
| Gm8566 | 20.28 | -3.84 | 0.00 |
| Gm7308 | 39.76 | -2.18 | 0.00 |
| Nrtn | 67.92 | -1.70 | 0.00 |
| Ftl1-ps1 | 39.87 | -2.59 | 0.00 |
| Rps3a2 | 68.11 | -2.81 | 0.00 |
| Rps18-ps5 | 20.63 | -4.20 | 0.00 |
| Rps27a-ps2 | 47.23 | -2.22 | 0.00 |
| Sap18b | 28.91 | -2.35 | 0.00 |
| Gm10288 | 88.85 | -3.43 | 0.00 |
| Gm49521 | 25.94 | 1.64 | 0.00 |
| Rps19-ps6 | 40.64 | -3.52 | 0.00 |
| Cox5b-ps | 36.04 | -2.45 | 0.00 |
| Gm8203 | 16.15 | -3.98 | 0.00 |
| Gm9816 | 30.43 | -2.93 | 0.00 |
| Gh | 843.07 | -10.52 | 0.00 |
| Rpl17-ps10 | 81.68 | -2.82 | 0.00 |
| Ube2srt | 18.59 | -2.95 | 0.00 |
| Rpl35rt | 119.88 | -3.71 | 0.00 |
| ENSMUSG00000121793 | 76.27 | -3.64 | 0.00 |
| Rpl34-ps1 | 79.62 | -6.35 | 0.00 |
| Rpl10a-ps1 | 61.21 | -1.82 | 0.00 |
| Gm15427 | 66.61 | -3.17 | 0.00 |
| Aldoart1 | 15.23 | -4.09 | 0.00 |
| Gm15772 | 25.37 | -3.13 | 0.00 |
| H2ac19 | 178.17 | -1.35 | 0.00 |
| Kcnmb4os1 | 36.92 | -2.68 | 0.00 |
| Gm12918 | 100.86 | -3.00 | 0.00 |
| Gm12254 | 20.16 | -2.62 | 0.00 |
| ENSMUSG00000121779 | 61.59 | -1.29 | 0.00 |
| Gm5436 | 13.85 | -3.91 | 0.00 |
| Prkcz2 | 29.28 | -2.60 | 0.00 |
| Gm11223 | 40.44 | -2.20 | 0.00 |
| Gm9385 | 43.98 | -3.23 | 0.00 |
| Gm8226 | 78.84 | -1.91 | 0.00 |
| Rps15a-ps7 | 14.61 | -3.49 | 0.00 |
| Gm8355 | 60.66 | -1.76 | 0.00 |
| ENSMUSG00000143433 | 23.78 | -3.48 | 0.00 |
| ENSMUSG00000137224 | 73.06 | -1.64 | 0.00 |
| Fbxl15 | 301.62 | -1.01 | 0.00 |
| Amn | 99.96 | -1.17 | 0.00 |
| Atp5pb-ps | 20.84 | -2.55 | 0.00 |
| Nme3 | 406.83 | -1.08 | 0.00 |
| Gm4332 | 28.61 | -4.64 | 0.00 |
| Gm38883 | 15.44 | -4.59 | 0.00 |
| Gm6789 | 40.74 | -1.99 | 0.00 |
| Hadhb-ps | 23.81 | -1.92 | 0.00 |
| Gm8730 | 23.56 | -3.20 | 0.00 |
| Gm10052 | 34.15 | -1.48 | 0.00 |
| Gm10073 | 42.10 | -3.92 | 0.00 |
| Rpl9-ps6 | 205.98 | -2.51 | 0.00 |
| Gm10163 | 42.91 | -2.14 | 0.00 |
| Rpl28-ps1 | 39.83 | -3.43 | 0.00 |
| Gm11478 | 40.63 | -3.68 | 0.00 |
| Gm7600 | 15.57 | -4.34 | 0.00 |
| Ywhaq-ps3 | 28.89 | -2.66 | 0.00 |
| Gm9616 | 12.73 | -3.42 | 0.00 |
| ENSMUSG00000124434 | 20.26 | -2.61 | 0.00 |
| Rpl3-ps1 | 172.77 | -1.90 | 0.00 |
| Rps10-ps2 | 42.88 | -2.09 | 0.00 |
| Gm37035 | 211.52 | -1.01 | 0.00 |
| Rpl17-ps3 | 51.36 | -3.14 | 0.00 |
| Rpl31-ps8 | 53.05 | -2.11 | 0.00 |
| Rpl19-ps11 | 98.62 | -2.73 | 0.00 |
| Rps16-ps2 | 57.35 | -3.14 | 0.00 |
| Gm6863 | 46.80 | -2.18 | 0.00 |
| ENSMUSG00000141748 | 74.57 | -1.59 | 0.00 |
| ENSMUSG00000121655 | 13.61 | -2.66 | 0.00 |
| ENSMUSG00000139771 | 129.19 | -3.08 | 0.00 |
| Gm13456 | 180.96 | -2.20 | 0.00 |
| Eno1b | 44.27 | -3.16 | 0.00 |
| Gm12251 | 12.81 | -3.41 | 0.00 |
| ENSMUSG00000138427 | 12.28 | -3.59 | 0.00 |
| Pgam1-ps2 | 72.13 | -2.81 | 0.00 |
| Eif4a-ps4 | 71.83 | -1.69 | 0.00 |
| ENSMUSG00000137056 | 11.14 | -3.02 | 0.00 |
| Gm8399 | 28.07 | -2.54 | 0.00 |
| Gm5537 | 109.46 | -2.16 | 0.00 |
| Uba52rt | 148.31 | -2.24 | 0.00 |
| Rps25-ps1 | 12.01 | -4.61 | 0.00 |
| Gm7666 | 20.71 | -3.19 | 0.00 |
| Gm14703 | 175.77 | -2.81 | 0.00 |
| Gm13611 | 10.47 | -5.35 | 0.00 |
| Gm45855 | 12.51 | -4.57 | 0.00 |
| ENSMUSG00000121783 | 428.90 | -1.68 | 0.00 |
| Gm6136 | 55.33 | -1.83 | 0.00 |
| Gm14494 | 11.31 | -2.92 | 0.00 |
| Rps24-ps3 | 28.76 | -3.44 | 0.00 |
| ENSMUSG00000123149 | 27.56 | -2.49 | 0.00 |
| Gm10053 | 130.76 | -2.69 | 0.00 |
| Gm9625 | 19.65 | -1.92 | 0.00 |
| 4930527F14Rik | 39.80 | -1.21 | 0.00 |
| Gm14121 | 10.39 | -2.82 | 0.00 |
| Gm6560 | 71.75 | -2.16 | 0.00 |
| Gm14150 | 18.23 | -2.84 | 0.00 |
| Glns-ps1 | 25.56 | -2.45 | 0.00 |
| Gm5499 | 26.45 | -2.14 | 0.00 |
| Gm9794 | 52.55 | -2.52 | 0.00 |
| Gm4202 | 63.44 | -1.78 | 0.00 |
| Gstp-ps | 13.24 | -3.34 | 0.00 |
| Actr3-ps | 17.22 | -2.37 | 0.00 |
| ENSMUSG00000121784 | 136.68 | -1.95 | 0.00 |
| ENSMUSG00000128633 | 86.75 | -4.38 | 0.00 |
| Gm12183 | 37.50 | -1.96 | 0.00 |
| Gm4366 | 83.48 | -2.26 | 0.00 |
| Gm10039 | 17.54 | -2.61 | 0.00 |
| Kansl2-ps | 10.47 | -2.96 | 0.00 |
| ENSMUSG00000121777 | 294.50 | -1.65 | 0.00 |
| 1810049J17Rik | 12.04 | -3.94 | 0.00 |
| Rpl36-ps12 | 24.73 | -2.47 | 0.00 |
| Gm6344 | 8.81 | -4.16 | 0.00 |
| Rplp2-ps1 | 21.23 | -4.61 | 0.00 |
| Rps27rt | 122.01 | -2.79 | 0.00 |
| Rpl18-ps2 | 19.29 | -3.18 | 0.00 |
| Eef2-ps2 | 17.43 | -2.56 | 0.00 |
| Gstm2-ps1 | 8.92 | -4.10 | 0.00 |
| Ap2m1-ps | 148.46 | -1.21 | 0.00 |
| A730035I17Rik | 34.80 | -1.66 | 0.00 |
| Gm12892 | 85.93 | -2.14 | 0.00 |
| ENSMUSG00000142490 | 15.19 | 3.15 | 0.00 |
| Adrm1b | 21.18 | -2.49 | 0.00 |
| Tmsb10b | 24.13 | -1.53 | 0.00 |
| Pcsk1n | 9172.98 | -1.04 | 0.00 |
| Atp6v0c-ps2 | 39.99 | -1.85 | 0.00 |
| Gm5422 | 13.37 | -3.08 | 0.00 |
| Rps23-ps1 | 43.83 | -2.53 | 0.00 |
| mt-Co2 | 48324.30 | -1.24 | 0.00 |
| Gm2999 | 17.14 | -2.94 | 0.00 |
| Gm12669 | 23.56 | -1.70 | 0.00 |
| Pomc | 219.02 | -3.31 | 0.00 |
| Vcp-rs | 48.11 | -1.54 | 0.00 |
| Gm5844 | 25.03 | -1.69 | 0.00 |
| Mif-ps4 | 9.36 | -4.22 | 0.00 |
| Gm16439 | 7.56 | -3.26 | 0.00 |
| Fam221b | 55.45 | -1.14 | 0.00 |
| ENSMUSG00000132147 | 11.74 | -3.28 | 0.00 |
| Ube2n-ps1 | 15.00 | -2.67 | 0.00 |
| Gm12346 | 127.56 | -1.54 | 0.00 |
| Nudc-ps1 | 12.10 | -2.31 | 0.00 |
| Gm56672 | 23.34 | -3.54 | 0.00 |
| Gm16437 | 12.88 | -2.43 | 0.00 |
| Gm7658 | 10.53 | -3.15 | 0.00 |
| Gm20431 | 112.10 | -6.85 | 0.00 |
| Gm2614 | 8.89 | -4.58 | 0.00 |
| Rps13-ps2 | 20.99 | -2.55 | 0.00 |
| Gm6204 | 30.40 | -4.01 | 0.00 |
| Tmem238 | 64.57 | -1.07 | 0.00 |
| Mxd4os1 | 28.54 | -1.09 | 0.00 |
| Gm2225 | 11.77 | -3.48 | 0.00 |
| Gm10250 | 43.79 | -2.51 | 0.00 |
| Arhgap27os2 | 11.76 | -2.11 | 0.00 |
| Oxt | 153.32 | -1.72 | 0.00 |
| Sms-ps | 16.46 | -2.00 | 0.00 |
| Gm16105 | 88.53 | 1.26 | 0.00 |
| Rpl6l | 18.78 | -2.20 | 0.00 |
| Gm7536 | 90.29 | -2.38 | 0.00 |
| ENSMUSG00000132287 | 18.32 | -2.60 | 0.00 |
| Nicol1 | 350.21 | -1.10 | 0.00 |
| Gm9493 | 36.54 | -2.81 | 0.00 |
| Rps18-ps6 | 38.82 | -3.38 | 0.00 |
| Hspe1-rs1 | 14.13 | -2.73 | 0.00 |
| Rpl7-ps7 | 6.39 | -3.32 | 0.00 |
| Ahcyl | 14.28 | -2.46 | 0.00 |
| Gm28901 | 62.18 | -1.00 | 0.00 |
| Gchfr | 23.93 | -1.65 | 0.00 |
| Gm3724 | 13.47 | -1.97 | 0.00 |
| Gm4459 | 11.14 | -2.75 | 0.00 |
| Pam16l | 10.51 | -2.69 | 0.00 |
| Gm10221 | 23.48 | -3.15 | 0.00 |
| Rps26-ps1 | 13.86 | -6.95 | 0.00 |
| Gm12174 | 19.91 | -2.62 | 0.00 |
| Rps15-ps2 | 9.49 | -3.20 | 0.00 |
| ENSMUSG00000126561 | 34.97 | -1.61 | 0.00 |
| Tpm3-rs7 | 18.15 | -1.87 | 0.00 |
| Pabpc1l2b | 14.98 | -7.06 | 0.00 |
| Cftr | 21.39 | 1.15 | 0.00 |
| Oaz1-ps | 65.74 | -2.28 | 0.00 |
| ENSMUSG00000131289 | 12.58 | -2.17 | 0.00 |
| Gm11964 | 4.98 | -4.25 | 0.00 |
| Rpl9-ps4 | 20.03 | -3.87 | 0.00 |
| Psma5-ps | 12.67 | -2.59 | 0.00 |
| Tpi-rs11 | 10.56 | -3.56 | 0.00 |
| Btf3-ps1 | 16.57 | -2.40 | 0.00 |
| Gm5421 | 16.88 | -2.26 | 0.00 |
| Nutf2-ps1 | 30.96 | -1.46 | 0.00 |
| Gm6055 | 11.02 | -3.01 | 0.00 |
| ENSMUSG00000125136 | 21.82 | -1.29 | 0.00 |
| Gm7730 | 3.19 | -4.81 | 0.00 |
| 2510046G10Rik | 15.90 | -1.43 | 0.00 |
| Gm15421 | 13.67 | -2.49 | 0.00 |
| Eef1a1-ps1 | 24.90 | -1.35 | 0.00 |
| ENSMUSG00000127515 | 11.16 | -2.01 | 0.00 |
| Gm5560 | 10.04 | -2.85 | 0.00 |
| Gm15519 | 5.33 | -3.76 | 0.00 |
| Gm5835 | 24.58 | -1.90 | 0.00 |
| Rps7-ps3 | 48.23 | -2.63 | 0.01 |
| ENSMUSG00000138717 | 15.30 | -2.50 | 0.01 |
| Gm15501 | 26.74 | -3.59 | 0.01 |
| Gm3571 | 7.39 | -3.84 | 0.01 |
| AK157302 | 15.86 | -2.08 | 0.01 |
| Gm3226 | 15.54 | -1.82 | 0.01 |
| Gm56991 | 52.52 | -1.47 | 0.01 |
| Erhrt-ps | 11.30 | -2.67 | 0.01 |
| Glo1-ps | 6.39 | -2.98 | 0.01 |
| Gm45051 | 15.47 | -1.51 | 0.01 |
| Rab11b-ps2 | 13.92 | -2.65 | 0.01 |
| APOE | 28177.85 | 2.11 | 0.01 |
| 4632415L05Rik | 9.66 | -6.42 | 0.01 |
| Gm10263 | 13.44 | -4.37 | 0.01 |
| ENSMUSG00000143530 | 6.95 | -2.45 | 0.01 |
| ENSMUSG00000132604 | 23.23 | -3.44 | 0.01 |
| Gm37123 | 5.34 | 2.17 | 0.01 |
| Gm13461 | 15.23 | -2.25 | 0.01 |
| Lbhd2 | 34.68 | -1.14 | 0.01 |
| Scand1 | 356.19 | -1.03 | 0.01 |
| Mrpl23-ps1 | 14.71 | -2.43 | 0.01 |
| 1600020E01Rik | 189.20 | -1.24 | 0.01 |
| Gm10642 | 37.78 | -1.46 | 0.01 |
| Gpi-ps | 55.85 | -2.14 | 0.01 |
| ENSMUSG00000123407 | 5.08 | -3.70 | 0.01 |
| Gm17167 | 34.44 | 3.78 | 0.01 |
| Gm21399 | 5.26 | -2.42 | 0.01 |
| Gm57848 | 39.85 | 1.26 | 0.01 |
| Gm13835 | 39.37 | -1.54 | 0.01 |
| Gm10819 | 14.98 | -2.31 | 0.01 |
| Ldhb-ps | 44.40 | -2.07 | 0.01 |
| Gm5905 | 14.34 | -2.74 | 0.01 |
| H3c15 | 37.44 | -1.05 | 0.01 |
| ENSMUSG00000122915 | 11.81 | -2.76 | 0.01 |
| Gm12966 | 16.76 | -1.65 | 0.01 |
| Gm21986 | 58.58 | -2.33 | 0.01 |
| Gm5424 | 11.62 | -2.10 | 0.01 |
| ENSMUSG00000125669 | 11.25 | -2.30 | 0.01 |
6.1.2.3 Females only
There are 265 significantly differentially expressed genes (FDR < 0.01, |log2FC| > 1) in the brain between female Cre-AAV and GFP control switch mice.
Diagnostic plots for the DE analysis
- A histogram enriched for low p-values shows the presence of true differential expression (deviation from the uniform null), rather than an all-noise result.
- The log(baseMean) distribution for significant genes being skewed toward moderate–high counts indicates findings are driven by well-expressed features, not low-count noise that can inflate fold-changes and p-values.
Significantly differentially expressed genes in brain
Cre-AAV and GFP control
(FDR < 0.01, |log2FC| > 1)
| gene | baseMean | log2FoldChange | padj |
|---|---|---|---|
| Rn7s1 | 578.80 | 2.53 | 0.00 |
| Gm22009 | 141.75 | 4.76 | 0.00 |
| Rn18s-rs5 | 236649.28 | 1.63 | 0.00 |
| Rn7sk | 507.70 | 2.20 | 0.00 |
| Lars2 | 30132.78 | 1.27 | 0.00 |
| Rpl35a-ps2 | 45.69 | -23.76 | 0.00 |
| Gm56350 | 30.27 | -23.13 | 0.00 |
| Gm49388 | 25.31 | -22.96 | 0.00 |
| Cdr1 | 107.69 | 1.82 | 0.00 |
| Gm15427 | 57.30 | -3.29 | 0.00 |
| Rpl19-ps11 | 101.22 | -2.82 | 0.00 |
| Gm11478 | 46.34 | -3.62 | 0.00 |
| Oaz1-ps | 60.14 | -2.85 | 0.00 |
| Rpl17-ps3 | 51.82 | -3.01 | 0.00 |
| Gm7536 | 100.26 | -2.78 | 0.00 |
| Rps16-ps2 | 55.74 | -3.60 | 0.00 |
| Rps7-ps3 | 50.66 | -3.34 | 0.00 |
| ENSMUSG00000140457 | 498.54 | 1.06 | 0.00 |
| Uba52rt | 142.29 | -2.30 | 0.00 |
| Gm4149 | 37.20 | -3.40 | 0.00 |
| Eno1b | 50.07 | -3.10 | 0.00 |
| Gm10073 | 41.72 | -3.90 | 0.00 |
| Gm5526 | 11.65 | -7.03 | 0.00 |
| Gpi-ps | 60.12 | -2.71 | 0.00 |
| Rps23-ps1 | 53.22 | -3.02 | 0.00 |
| Rpl3-ps1 | 183.86 | -1.94 | 0.00 |
| Gm4366 | 76.23 | -2.33 | 0.00 |
| B020010K11Rik | 35.08 | -3.08 | 0.00 |
| Rpsa-ps10 | 71.75 | -2.89 | 0.00 |
| Gm12892 | 87.07 | -2.61 | 0.00 |
| Tpt1-ps3 | 60.04 | -2.57 | 0.00 |
| Rps19-ps6 | 37.77 | -3.76 | 0.00 |
| Cox5b-ps | 35.77 | -2.97 | 0.00 |
| Rpl34-ps1 | 28.65 | -4.33 | 0.00 |
| Rps18-ps5 | 22.58 | -5.55 | 0.00 |
| Rpl18-ps2 | 18.60 | -5.55 | 0.00 |
| ENSMUSG00000121784 | 148.22 | -2.03 | 0.00 |
| Gm9493 | 25.84 | -3.09 | 0.00 |
| Rpl35rt | 137.02 | -3.73 | 0.00 |
| Gm9385 | 44.07 | -2.78 | 0.00 |
| Rpl17-ps10 | 72.91 | -2.68 | 0.00 |
| Gm8226 | 76.06 | -1.91 | 0.00 |
| ENSMUSG00000128633 | 88.74 | -3.90 | 0.00 |
| Gm4202 | 66.20 | -1.74 | 0.00 |
| Rps18-ps6 | 35.64 | -3.35 | 0.00 |
| Rps6-ps4 | 116.79 | -1.96 | 0.00 |
| Rps24-ps3 | 25.65 | -3.03 | 0.00 |
| ENSMUSG00000132604 | 23.11 | -3.60 | 0.00 |
| ENSMUSG00000143433 | 24.05 | -4.55 | 0.00 |
| Gm16437 | 14.40 | -3.97 | 0.00 |
| Gm12481 | 45.88 | -7.82 | 0.00 |
| Gm6560 | 70.09 | -2.32 | 0.00 |
| Gm4332 | 26.52 | -3.81 | 0.00 |
| 1810049J17Rik | 15.50 | -4.71 | 0.00 |
| mt-Co2 | 58270.43 | -1.22 | 0.00 |
| Rpl14-ps1 | 55.66 | -2.75 | 0.00 |
| Gm15772 | 30.85 | -3.25 | 0.00 |
| Malat1 | 18026.65 | 1.98 | 0.00 |
| Ldhb-ps | 45.47 | -2.21 | 0.00 |
| Rps3a2 | 69.23 | -2.80 | 0.00 |
| Rps13-ps1 | 28.55 | -3.68 | 0.00 |
| Pcsk1n | 9963.48 | -1.11 | 0.00 |
| Gm14586 | 30.02 | -3.35 | 0.00 |
| Gm12174 | 16.50 | -3.85 | 0.00 |
| Gm9794 | 54.91 | -2.29 | 0.00 |
| Pgam1-ps2 | 64.52 | -2.52 | 0.00 |
| Rpl28-ps1 | 36.76 | -2.66 | 0.00 |
| Nicol1 | 368.74 | -1.22 | 0.00 |
| Nme3 | 454.49 | -1.08 | 0.00 |
| Gm4459 | 10.91 | -3.78 | 0.00 |
| Gm5499 | 27.49 | -2.64 | 0.00 |
| Fbxl15 | 319.39 | -1.05 | 0.00 |
| ENSMUSG00000121779 | 75.07 | -1.60 | 0.00 |
| Gm10053 | 144.97 | -2.71 | 0.00 |
| H2aj | 808.32 | -1.05 | 0.00 |
| ENSMUSG00000128869 | 20.02 | -3.77 | 0.00 |
| Rps25-ps1 | 14.79 | -4.19 | 0.00 |
| Rpl31-ps8 | 55.61 | -2.02 | 0.00 |
| Scand1 | 383.28 | -1.20 | 0.00 |
| Gm10250 | 38.72 | -2.38 | 0.00 |
| Rps10-ps2 | 41.75 | -2.20 | 0.00 |
| ENSMUSG00000137224 | 93.43 | -1.85 | 0.00 |
| Gm2225 | 15.75 | -3.89 | 0.00 |
| Gm10221 | 18.99 | -3.22 | 0.00 |
| Atp6v0c-ps2 | 37.49 | -2.07 | 0.00 |
| Gm6204 | 26.63 | -3.69 | 0.00 |
| Gm8730 | 21.54 | -4.27 | 0.00 |
| Btf3l4b | 22.29 | -1.95 | 0.00 |
| Gm10288 | 103.00 | -3.13 | 0.00 |
| Nr2f6 | 642.28 | -1.00 | 0.00 |
| Ap2m1-ps | 153.71 | -1.40 | 0.00 |
| Nudc-ps1 | 12.83 | -3.19 | 0.00 |
| Rpl9-ps6 | 208.43 | -2.43 | 0.00 |
| Gm37811 | 58.51 | -1.77 | 0.00 |
| ENSMUSG00000135935 | 65.49 | 6.02 | 0.00 |
| Gm13436 | 26.37 | -3.63 | 0.00 |
| Vcp-rs | 48.71 | -1.96 | 0.00 |
| Rpl6l | 21.80 | -2.32 | 0.00 |
| Glns-ps1 | 29.13 | -3.00 | 0.00 |
| Eef2-ps2 | 16.08 | -3.65 | 0.00 |
| ENSMUSG00000121793 | 90.21 | -3.07 | 0.00 |
| Rps27rt | 133.38 | -2.82 | 0.00 |
| Gm6789 | 38.76 | -2.16 | 0.00 |
| ENSMUSG00000138136 | 23.55 | -2.07 | 0.00 |
| ENSMUSG00000139771 | 156.48 | -3.15 | 0.00 |
| 9530059O14Rik | 33.09 | 1.86 | 0.00 |
| Fam221b | 61.82 | -1.33 | 0.00 |
| Gm8566 | 19.16 | -2.80 | 0.00 |
| Gm13456 | 190.04 | -2.47 | 0.00 |
| Gm13835 | 46.99 | -1.89 | 0.00 |
| Gm44442 | 149.19 | -1.81 | 0.00 |
| ENSMUSG00000126438 | 9.67 | -4.74 | 0.00 |
| H3c15 | 43.23 | -1.43 | 0.00 |
| Gm37035 | 236.47 | -1.27 | 0.00 |
| ENSMUSG00000131289 | 11.99 | -2.86 | 0.00 |
| Gm2223 | 21.79 | -2.19 | 0.00 |
| Gm5805 | 11.79 | -4.29 | 0.00 |
| Gm13611 | 9.21 | -6.08 | 0.00 |
| Gm5436 | 13.44 | -3.74 | 0.00 |
| Gm10263 | 11.86 | -4.65 | 0.00 |
| Gm11223 | 36.70 | -2.13 | 0.00 |
| Gm37899 | 20.43 | 2.35 | 0.00 |
| Gm7600 | 17.47 | -4.26 | 0.00 |
| Hspe1-rs1 | 14.06 | -3.89 | 0.00 |
| Endog | 314.93 | -1.05 | 0.00 |
| ENSMUSG00000138427 | 16.21 | -3.65 | 0.00 |
| Gm49325 | 122.37 | 1.01 | 0.00 |
| Gm12346 | 130.36 | -1.12 | 0.00 |
| ENSMUSG00000121777 | 292.85 | -1.95 | 0.00 |
| Rps27a-ps2 | 47.55 | -2.18 | 0.00 |
| Gm6863 | 45.00 | -2.05 | 0.00 |
| Gm21986 | 68.28 | -1.64 | 0.00 |
| Gm13680 | 10.46 | -2.97 | 0.00 |
| Actr3-ps | 18.75 | -2.38 | 0.00 |
| 4933431K14Rik | 76.28 | -1.06 | 0.00 |
| Gm12350 | 18.05 | -3.16 | 0.00 |
| Gm7308 | 38.06 | -2.11 | 0.00 |
| Rn7s2 | 77.59 | 9.68 | 0.00 |
| Tmem238 | 66.11 | -1.10 | 0.00 |
| Hadhb-ps | 30.08 | -1.50 | 0.00 |
| Rps15a-ps7 | 16.15 | -3.10 | 0.00 |
| Rps10-ps1 | 14.11 | -3.94 | 0.00 |
| Gm13461 | 14.94 | -2.68 | 0.00 |
| Gm45855 | 13.17 | -3.60 | 0.00 |
| Kcnq1ot1 | 382.85 | 1.02 | 0.00 |
| Rpl37rt | 34.71 | -8.60 | 0.00 |
| Eif4a-ps4 | 80.28 | -1.36 | 0.00 |
| Gm3571 | 8.06 | -4.83 | 0.00 |
| Gm10052 | 39.44 | -1.60 | 0.00 |
| Rpl10a-ps1 | 67.61 | -1.53 | 0.00 |
| Rpl9-ps4 | 24.26 | -2.76 | 0.00 |
| ENSMUSG00000121655 | 12.87 | -2.72 | 0.00 |
| Erhrt-ps | 13.16 | -3.67 | 0.00 |
| Gm5424 | 13.49 | -2.69 | 0.00 |
| Rps15-ps2 | 9.91 | -3.50 | 0.00 |
| Mif-ps4 | 12.67 | -4.79 | 0.00 |
| Gm8355 | 55.12 | -1.52 | 0.00 |
| Gm8203 | 16.03 | -2.70 | 0.00 |
| Gm10036 | 11.59 | -3.51 | 0.00 |
| Gm9816 | 26.01 | -2.34 | 0.00 |
| Gm5835 | 21.97 | -2.14 | 0.00 |
| Gm2614 | 7.74 | -3.94 | 0.00 |
| Gm13066 | 16.48 | -3.17 | 0.00 |
| mt-Ts1 | 6.47 | -5.57 | 0.00 |
| 4632415L05Rik | 19.89 | -7.80 | 0.00 |
| Gm5421 | 15.84 | -2.24 | 0.00 |
| Yjefn3 | 131.82 | -1.21 | 0.00 |
| Gm8399 | 33.76 | -2.03 | 0.00 |
| Rab11b-ps2 | 12.32 | -2.56 | 0.00 |
| Gm9625 | 25.86 | -1.92 | 0.00 |
| Gstp-ps | 13.73 | -3.23 | 0.00 |
| Gm42583 | 29.71 | 2.14 | 0.00 |
| Gm7816 | 22.67 | -2.32 | 0.00 |
| Nrtn | 73.39 | -1.73 | 0.00 |
| Gm7666 | 19.23 | -2.84 | 0.00 |
| Gm6136 | 48.86 | -1.53 | 0.00 |
| ENSMUSG00000123407 | 4.74 | -5.12 | 0.00 |
| Gm12254 | 18.46 | -2.09 | 0.00 |
| ENSMUSG00000123314 | 87.48 | -1.24 | 0.00 |
| Rpl36a-ps2 | 18.97 | -2.25 | 0.00 |
| Gm14150 | 18.33 | -2.82 | 0.00 |
| Aldoart1 | 15.76 | -2.96 | 0.00 |
| Mrpl23-ps1 | 14.71 | -3.54 | 0.00 |
| Cdk2ap1rt | 43.71 | -1.83 | 0.00 |
| Crlf2 | 282.80 | -1.02 | 0.00 |
| Gm11175 | 17.39 | -1.75 | 0.00 |
| Gm2999 | 18.90 | -2.59 | 0.00 |
| Rpl23a-ps3 | 33.27 | -2.58 | 0.00 |
| Rpph1 | 25.44 | 1.96 | 0.00 |
| Rps26-ps1 | 14.33 | -7.33 | 0.00 |
| Gal | 89.53 | -1.06 | 0.00 |
| Ube2srt | 24.01 | -2.52 | 0.00 |
| Gm10819 | 16.58 | -2.68 | 0.00 |
| Gm9531 | 12.27 | -2.56 | 0.00 |
| Rpl7-ps7 | 6.87 | -3.17 | 0.00 |
| Gm37530 | 13.26 | 2.12 | 0.00 |
| ENSMUSG00000138717 | 20.46 | -1.93 | 0.00 |
| Gadd45g | 397.60 | -1.05 | 0.00 |
| Gm5905 | 18.63 | -2.68 | 0.00 |
| Gm6180 | 23.98 | -2.06 | 0.00 |
| Sap18b | 31.02 | -2.11 | 0.00 |
| Gm9824 | 28.37 | -1.77 | 0.00 |
| ENSMUSG00000132287 | 13.72 | -3.34 | 0.00 |
| Gm12183 | 40.77 | -1.95 | 0.00 |
| Kcng3 | 28.31 | 1.19 | 0.00 |
| Btf3-ps1 | 13.70 | -2.15 | 0.00 |
| ENSMUSG00000139219 | 17.51 | 1.76 | 0.00 |
| Gm10163 | 49.84 | -1.60 | 0.00 |
| Cox7a1 | 40.34 | -1.02 | 0.00 |
| Gm6170 | 7.76 | -4.30 | 0.00 |
| ENSMUSG00000140944 | 15.50 | -2.30 | 0.00 |
| Zfp781a | 61.15 | 1.05 | 0.00 |
| ENSMUSG00000121783 | 451.50 | -1.43 | 0.00 |
| Gm14121 | 12.44 | -2.59 | 0.00 |
| Gm6344 | 10.55 | -3.14 | 0.00 |
| Gm56991 | 65.25 | -1.27 | 0.00 |
| Hmgn2-ps | 138.07 | -1.05 | 0.00 |
| Mrip-ps | 13.92 | -2.09 | 0.00 |
| Gm12251 | 10.37 | -2.88 | 0.00 |
| Gm12966 | 17.33 | -1.95 | 0.00 |
| Gm2423 | 24.69 | -2.28 | 0.00 |
| Gm9755 | 9.72 | -2.78 | 0.00 |
| Gm5844 | 27.67 | -1.54 | 0.00 |
| Tmsb10b | 26.00 | -1.76 | 0.00 |
| G630016G05Rik | 112.76 | 1.10 | 0.00 |
| Eif3j2 | 21.21 | -2.10 | 0.00 |
| ENSMUSG00000121782 | 4.70 | -4.45 | 0.01 |
| Gm16439 | 9.53 | -2.92 | 0.01 |
| Gm37310 | 20.42 | 1.46 | 0.01 |
| D830035M03Rik | 19.33 | -1.43 | 0.01 |
| Gm11964 | 6.48 | -3.88 | 0.01 |
| 1700034P13Rik | 49.33 | 1.67 | 0.01 |
| Gm5456 | 4.30 | -4.97 | 0.01 |
| Nutf2-ps1 | 35.09 | -1.50 | 0.01 |
| Gstm2-ps1 | 10.97 | -3.16 | 0.01 |
| Gm15519 | 6.53 | -3.13 | 0.01 |
| Gm12918 | 86.65 | -2.99 | 0.01 |
| H2ac19 | 228.40 | -1.62 | 0.01 |
| Adrm1b | 15.11 | -1.84 | 0.01 |
| Pglyrp1 | 178.11 | -1.02 | 0.01 |
| Col6a5 | 12.20 | 2.09 | 0.01 |
| Gm44170 | 36.56 | -2.14 | 0.01 |
| Tpm3-rs7 | 20.05 | -1.76 | 0.01 |
| Gm14494 | 14.32 | -1.97 | 0.01 |
| 5730405O15Rik | 22.94 | 1.25 | 0.01 |
| Hspd1-ps3 | 18.08 | -1.91 | 0.01 |
| Rpl36-ps12 | 24.74 | -2.19 | 0.01 |
| Avp | 269.53 | -1.45 | 0.01 |
| Scp2-ps2 | 5.67 | -3.77 | 0.01 |
| Gm10039 | 13.74 | -2.24 | 0.01 |
| ENSMUSG00000140290 | 28.88 | -1.33 | 0.01 |
| Tpi-rs11 | 11.26 | -3.46 | 0.01 |
| Impdh2-ps | 9.35 | -2.45 | 0.01 |
| ENSMUSG00000136525 | 53107.71 | 1.97 | 0.01 |
| Gm57504 | 53.53 | -1.11 | 0.01 |
| Gm43843 | 48.27 | 1.44 | 0.01 |
| Ube2n-ps1 | 16.58 | -2.23 | 0.01 |
| Prkcz2 | 28.06 | -1.73 | 0.01 |
| Ccdc171 | 34.14 | 1.04 | 0.01 |
| 4921516A02Rik | 14.38 | -2.85 | 0.01 |
| ENSMUSG00000129048 | 35.44 | 1.78 | 0.01 |
| ENSMUSG00000133032 | 12.16 | 2.10 | 0.01 |
| Ahcyl | 13.11 | -2.55 | 0.01 |
| ENSMUSG00000129696 | 20.90 | 1.14 | 0.01 |
| Gm56769 | 28.84 | -1.66 | 0.01 |
6.1.2.4 Common DEGs in males and females
Differential expression analysis comparing Cre-AAV and GFP control groups in brain identified a large number of significantly altered transcripts (FDR < 0.01, |log₂FC| > 1). To focus on robust and biologically relevant signals, we intersected DEGs detected in both male and female mice.
There were 178 common DEGs shared in male and females. The majority corresponded to ribosomal and uncharacterized pseudogenes, reflecting global transcriptional perturbations rather than specific pathway activation.
| gene |
|---|
| Gm16437 |
| Fbxl15 |
| Tmem238 |
| Pcsk1n |
| Nrtn |
| Adrm1b |
| Gm5436 |
| Gpi-ps |
| Gm6863 |
| Fam221b |
| Oaz1-ps |
| Gm8399 |
| Gm9493 |
| Ldhb-ps |
| Scand1 |
| Gm11223 |
| Gm5424 |
| Rpl14-ps1 |
| Rpsa-ps10 |
| Gm8566 |
| Ahcyl |
| 4632415L05Rik |
| Rps27rt |
| Gm6180 |
| Rpl18-ps2 |
| Gm7536 |
| Tpm3-rs7 |
| Rpl28-ps1 |
| Rps27a-ps2 |
| Gm10052 |
| Gm10053 |
| Eno1b |
| Aldoart1 |
| Rps26-ps1 |
| Gm10073 |
| Rps16-ps2 |
| Sap18b |
| Gm15772 |
| Rpl9-ps6 |
| Rps3a2 |
| Erhrt-ps |
| Hadhb-ps |
| Gm8730 |
| H2ac19 |
| mt-Co2 |
| Gm13611 |
| Gm12918 |
| Rps13-ps1 |
| Gm10263 |
| Gm10163 |
| Rps25-ps1 |
| Gm7666 |
| Gm10221 |
| Rpl31-ps8 |
| Uba52rt |
| Rpl34-ps1 |
| Gm10250 |
| Rps18-ps6 |
| Gm10288 |
| Gm12966 |
| Nicol1 |
| Gm5499 |
| Rps15-ps2 |
| Nutf2-ps1 |
| Gm16439 |
| Nme3 |
| Gm4149 |
| Gm10819 |
| Mrpl23-ps1 |
| Rpl23a-ps3 |
| Rpl35rt |
| Cox5b-ps |
| Atp6v0c-ps2 |
| Gm12174 |
| Gm9385 |
| Gm11964 |
| Rps24-ps3 |
| Gm15427 |
| H3c15 |
| Rps15a-ps7 |
| Rpl19-ps11 |
| Gm7308 |
| Ap2m1-ps |
| Rps6-ps4 |
| Rpl17-ps10 |
| Gm13461 |
| Pgam1-ps2 |
| Glns-ps1 |
| Actr3-ps |
| Gm12183 |
| Gm13456 |
| Eef2-ps2 |
| Gm14150 |
| Gm5844 |
| Gm14494 |
| Gm14121 |
| Vcp-rs |
| Gm15519 |
| Gm14586 |
| Gm4459 |
| Mif-ps4 |
| Gm12892 |
| Gm13436 |
| Gm12346 |
| Gm11478 |
| Gm6136 |
| Rpl3-ps1 |
| Gm12251 |
| Rpl10a-ps1 |
| Gm12254 |
| Gm9816 |
| Gm13835 |
| Btf3-ps1 |
| Gm3571 |
| Rpl6l |
| Gm4202 |
| Gm10039 |
| Rpl36-ps12 |
| Tmsb10b |
| Gm8355 |
| Gm6344 |
| Rpl9-ps4 |
| Rps7-ps3 |
| Rab11b-ps2 |
| Gm21986 |
| Rps19-ps6 |
| 1810049J17Rik |
| Gm5421 |
| Gm9625 |
| Rps10-ps2 |
| Gm8226 |
| Rps23-ps1 |
| Eif4a-ps4 |
| Gm5835 |
| Gm8203 |
| Gm37035 |
| Gm56350 |
| Gstp-ps |
| Gm6560 |
| Rpl36a-ps2 |
| Gm6204 |
| Gm4332 |
| Tpi-rs11 |
| Ube2n-ps1 |
| Rpl7-ps7 |
| Gm9794 |
| Gstm2-ps1 |
| Gm4366 |
| Prkcz2 |
| Gm7600 |
| Gm2225 |
| Gm5905 |
| Nudc-ps1 |
| Gm45855 |
| Rps18-ps5 |
| Gm2614 |
| Rpl17-ps3 |
| Gm2999 |
| Hspe1-rs1 |
| Gm6789 |
| Ube2srt |
| Gm56991 |
| ENSMUSG00000121655 |
| ENSMUSG00000121777 |
| ENSMUSG00000121779 |
| ENSMUSG00000121783 |
| ENSMUSG00000121784 |
| ENSMUSG00000121793 |
| ENSMUSG00000123407 |
| ENSMUSG00000128633 |
| ENSMUSG00000131289 |
| ENSMUSG00000132287 |
| ENSMUSG00000132604 |
| ENSMUSG00000137224 |
| ENSMUSG00000138427 |
| ENSMUSG00000138717 |
| ENSMUSG00000139771 |
| ENSMUSG00000143433 |
Filtering out pseudogenes, unannotated loci (Gm*), mitochondrial genes, and Ensembl-only identifiers yielded 25 high-confidence nuclear genes consistently dysregulated across sexes, representing the shared brain response to Cre-mediated ApoE4→ApoE2 conversion.
Fbxl15, Tmem238, Pcsk1n, Nrtn, Adrm1b, Fam221b, Scand1, Ahcyl, 4632415L05Rik, Tpm3-rs7, Eno1b, Aldoart1, Sap18b, H2ac19, Uba52rt, Nicol1, Nme3, H3c15, Vcp-rs, Tmsb10b, 1810049J17Rik, Tpi-rs11, Prkcz2, Hspe1-rs1, Ube2srtThe set included genes involved in proteostasis and ubiquitin signaling (Adrm1b, Uba52rt, Ube2srt, Vcp-rs, Hspe1-rs1), cytoskeletal organization (Tpm3-rs7, Tmsb10b), and energy metabolism (Eno1b, Aldoart1, Tpi-rs11). Additional changes were observed in genes implicated in neuronal signaling and synaptic modulation, including Nrtn (neurturin), Pcsk1n, Ahcyl, and Prkcz2.
Several of these transcripts (Adrm1b, Eno1b, Sap18b, Vcp-rs, Hspe1-rs1) overlapped with those altered in the liver, indicating a shared transcriptional response to ApoE2 expression.